PuzzleRun Mac OS

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ANT RUN PRO is a fast paced arcade game where your goal is to keep the ant running through the ant tunnels. You only have 8 seconds before the ant will emerge from the starting hole and begin racing through the tunnels. Note: If you choose Cash/Check registration you will fill out your information online, print out your confirmation and mail it in with your payment.

Sherlock.

What user-support person, when seeing the message produced when a new game is started in Sherlock - The Game of Logic.

. wouldn't say to himself (or herself) 'Oh! Don't I wish!'

A friend sent me a copy of this game and, for me, it rapidly becameaddictive. I have since found the web site of the author, Everett Kaserand registered the game. I also found there is a newer version that addsa few more features such as saving an incompletely-solved game to continuelater and shelling to DOS. (Unfortunately, the 'Shell to DOS' onlyworks if your shell is COMMAND.COM. It does not work with 4DOS.)From Everett Kaser's web site:

Sherlock is a computerized version of logic puzzles, where you're presented with a series of clues that help you to determine the exact locations of 36 different images in a 6 x 6 array. Each of 6 rows contain 6 different images of the same type (faces, houses, numbers, fruit, street signs, or the letters 'HOLMES'). The computer scrambles the locations of the items in each row (without showing you their locations) and then presents to you a set of graphical clues that describe the physical relationships of different images. You use the clues to deduce where things can't be (and where they HAVE to be) until you know where all of the images are located.

Here is what the game looks like at the beginning of play:

Sherlock is shareware available fromEverett Kaser Software andthe MS-DOS version can be downloaded from Everett'sMSDOS Games page.A Windows version is also available and when I registered the MS-DOS versionI received registered versions of both the MS-DOS and Windows versions.(His site also has other games and puzzles and quite a few puzzlelinks. Fans of FreeCell will find one link especially interesting.)

Note: The game requires a mouse.

Problems:

There are a few minor annoyances to the older version of the game:

  • A few games in the old version generate too many clues and not all are visible. This can mean that you may have to guess at two or more possible solutions to the visible clues to get the right one. This is fixed in the newer version.
  • Once in a long while the screen appears to freeze during the 'fireworks' display at the end of a won game. This is because one of the images which is supposed to move across the screen at a random velocity and explode when it hits the edge of the screen gets a random velocity of zero. You can press the right mouse button or the ESC key to abort the display and restore the menu but it can be disconcerting when you first encounter this. The current version doesn't appear to be afflicted with this problem -- especially since the current version can be run in a mode that continuously displays the 'win' display (now one of three patterns to choose from). If the freeze problem still existed then it would have shown up long ago.
  • When you load new images, the new full sized images take effect immediately. The thumbnails are not changed until you exit the game and restart it with the new images as the default. This appears to be fixed in the new version.
  • When you edit the images and wish to save your changes, you must specify the file name without the extension. With the new version of the game, if you used the file-open menu to load an image file for editing, the default name in the Save prompt is the name of the file loaded with the extension. You have to delete the extension or the save will fail.
  • With the default set of images, it is hard to tell some of the images apart when you are using a VGA monochrome monitor. It may be necessary to edit the images (especially the coloured houses) to make the images look different from each other. You can also get a different set of images -- see below.

A problem in the new game:

  • If you use the 'Save Game' feature in the new version (notavailable in the old version) and forget to load your mouse driver after alater reboot before running Sherlock there is no way to exit from the gamewithout Sherlock thinking you want to abandon the saved game so the savedgame is deleted. So, if your mouse driver is not automatically loaded atbootup time, don't forget to load it before running Sherlock if you have asaved game. I plan to experiment with a batch file to see if I can detectthe absense of a mouse driver and prompt for one before running Sherlock.Stay tuned.

Running Sherlock with a monochrome monitor:

I found it difficult enough to tell some of the default images apartwith a monochrome monitor that I created my own sets of images which youcan download as a single zipped package. (As abonus, I am including a copy of the original default images touched up tomake them more usable with monochrome monitors. They probably lookhorrible with colour monitors.) You might prefer using one ofthose. They are (in order of difficulty in solving one of the logicproblems):

  1. A set of 36 images consisting of the digits '0' to '9' and the letters 'A' to 'Z'.
  2. A set of six geometrical shapes (oval, diamond, rectangle, dotted oval(one tiny oval inside another), dotted diamond, and dotted rectangle) withthe six possible combinations of black, white, and coloured (which appearsgrey on my screen). Each row has one shape with all six colour combinations.
  3. A set of the same geometrical shapes as above but with one of each shapeAND one of each colour combination in each row.

The game shown above using the default images is shown below with each ofmy three custom image sets:

The Alpha-Numeric set:
On a colour screen:
On a monochrome screen:

The Geometric Shapes, one shape per row:
On a colour screen:
On a monochrome screen:

The Geometric Shapes, all six shapes in each row:
On a colour screen:
On a monochrome screen:

New Coloured Image Sets:

For those with coloured monitors who may prefer more different colours,I have converted my Geometric Shapes to use six colours plus black (and,in two cases, white) instead of just black, white, and blue. You can graba set of various slightly-different versions as a zipped package calledgeo-col.zip and pick the variation youprefer.

For an even more eye-watering set and one that might causecerebral-meltdown, try my 'PIPES?.SHI' set which hasfour colours with all possible two-colour pairings (twelve of them)with three different shapes (plus black for a background and grey for the border). That image set is a filecalled pipes.zip but be warned, you need to bevery careful when you use it because it is very easy to makemistakes. There are three versions -- pipes1.shi with a thick (two-pixelwide) border, pipes2.shi with a one-pixel border, and pipes3.shi withno border at all (which makes it very difficult).

Note, if you grabbed an earlier version of pipes.zip, you might havegotten the first copy I put up here. That one was buggy. I accidentallygot the colours reversed on one image (blue and green instead of green andblue) making that image the same as another. Grab the new pipes.zip forthe corrected version.

The PIPES*.SHI files were not difficult enough for you? Try mySPOTS.SHI file, also available as a zipped file(but be sure to be wearing sunglasses or you'll be seeing spots forhours). [NEW] The zip-file now includes SPOTS-M.SHI for users withmonochrome monitors.

A quick-and-dirty screen-saver.

The new version of Sherlock can be run in a demo mode that displays acontinously running show of the screen display that you usually see aftera winning game. If a set of inages is edited so that most of them areblack and just a few are coloured, running Sherlock with the'-bf' switch,
C:>sherlock -bf
then you have a very effective and colourful screen-saver that rivalsome of the more flamboyant Windows screen-savers. One such editedset of images,sher-ss.zip, can be downloaded here andunzipped. That set is terrible for playing Sherlock, however.☺

Do you find Sherlock too easy?

If an orderly matrix of shapes makes solving things too easy, you couldtry scrambling the images. (I recommend copying the set to be scrambled toa file called TEMP.SHI and make that your Sherlock default image set. Thenyou can scramble TEMP.SHI as often as you want without fouling up theoriginal image sets.) To allow others to scramble their images, I havecreated another zipped package that uses DEBUGscripts to re-arrange the images in an image set in a (pseudo-)randomfashion. For 4DOS users, there is a BTM file that creates a newrandomly-generated DEBUG script on the fly to mix up the images. Forthose using COMMAND.COM, there is a BAT file which allows you to manuallychoose one of ten DEBUG scripts (originally randomly-generated) formixing the images.

Sherlock image set for anti-spammers.

I have a Sherlock image set for antispammers with the newsgroup,news.admin.net-abuse.email in five colours plus 'NOSPAM' in red and pink.Other images include 'UCE', 'TINLC', 'rDNS', 'C&C', White and Black hats(instead of the '.' box), and 'LART' (instead of the slashed circle).It's in a file named nanaeshi.zip and includesthe images plus an HTML file with links to information or definitions forthe newsgroup and terms mentioned above. Anti-spammers, have fun.

Two additional games you can play with Sherlock:

Do you have younger children who would like to play games with your computerbut don't have the logical skills for playing Sherlock? Using the rightSherlock image sets and the Sherlock quilt 'win' screen, there are twosimple games that can be played.

Word Seek.

Instructions:

  1. Set Sherlock to use my ALPHANUM.SHI image set with the 26 letters ofthe alphabet and the ten digits (part ofshapes.zip mentioned above). You can either usethe Sherlock 'Load Image Set' feature to select it or do as I do, setSherlock to use a temporary file name (I use 'test.shi') and then usethe DOS COPY command to copy the wanted image set to the temporary file.
  2. Run Sherlock with the command:
    sherlock -bq
    to get it to display the changing quilt pattern.
  3. Press the Pause key to freeze the display.
  4. Try to find as many words as you can that can be made by tracing fromone horizontally, vertically, or diagonally adjacent letter to another.(The individual words need not be adjacent.)
  5. Make up a point system that rewards the most words found, the longestwords found, etc. Set the minimum word length to two, three, four, ormore to adjust for different children's reading level. I am not settingany hard rules here because you know your children better than I do.
  6. Press some other key (the Enter key or the space bar are goodones to use) to unfreeze the display and then press Pause againfor another search with new letters.
  7. Repeat the steps above, quitting before boredom sets in.

View or download a typical screen-shot of Word Seek.

Plumbing.

Use the same method of play as above except using my PIPES3.SHI image set(part of pipes.zip mentioned above).In this case, you are looking for:

  1. A twisty, multicoloured path that leads fron one edge of the board tothe opposite edge. Bonus points for a path that connects from the left-handedge of the screen to the right-hand edge (because it is longer andless-frequently possible). Extra points for the longest path from eitherleft to right or top to bottom. Again, invent your own point system.
  2. Closed loops that don't touch the edge at all. (The shortest possibleis one that goes through four squares.) Long ones may be found thattwist and turn and finally return to the arbitrary starting square. Bonusescan be scored for the longest closed path too.

View or download a typical screen-shot of Plumbing.

Chip's Challenge.

One game that started on the Atari Lynx game machine and then got ported toWindows and included in their 'Entertainment Pack' (sadly no longeravailable (legally)) by Microsoft is Chip's Challenge.There is a whole community of Chip's Challenge players.There is even a (GPLed, if I'm not mistaken) duplicate of Chip's Challengeavailable (with different graphics for copyright reasons and supportingboth the Lynx Gameboy behaviour and the slightly different Microsoftbehaviour of the game) called Tile World. Bovada casino no deposit bonus.

Here are some Chip's Challenge links and related games from mybookmarks, sorted by URL to remove duplicates:

http://a_magical_me.home.comcast.net/chip/chip.html
Andrew's Tech Site [including Chip's Challenge]
http://ca.geocities.com/andy_tek/
Chip's Challenge Portal
http://ca.geocities.com/andy_tek/cc_portal/
ChipEnd
http://ca.geocities.com/andy_tek/andrews_software/apps/chips_utils/chipend/
CCTools Home
http://cctools.translucentdragon.com/main.htm
The Official CCTools webpage
http://cctools.translucentdragon.com/
c4 - Chip's Challenge combined converter
http://chips.kaseorg.com/pub/chips/c4.html
The Chip's Challenge Corridor - Other files
http://chips.kaseorg.com/solutions/other.php
The Chip's Challenge Corridor - FAQ - Tile World
http://chips.kaseorg.com/faq/cache/18.html
Mike L's Chip's Challenge Site
http://chips.pillowpc2001.net/
Chip's Controls
http://chips.pillowpc2001.net/controls/
Chip's DacGen
http://chips.pillowpc2001.net/dacgen.htm
Resources for MikeL2 (Mike's level set)
http://chips.pillowpc2001.net/MikeL2/
MikeL2 AVIs
http://chips.pillowpc2001.net/MikeL2/avis.htm
Escape : Free Puzzle game for Windows, Linux, Mac OSX
(similar to Chip's Challenge)
http://escape.spacebar.org/
Download ML Maze
(another game similar to Chip's Challenge)
http://mlmaze.pillowpc2001.net/download.htm
ml.pillowpc2001.net - Mike L's Web Site
http://ml.pillowpc2001.net/
Chip's Challenge Level Pack 2
http://www.agt.net/public/nfield/ChipChallenge/CCLP2.html
pieguy's Chip's Challenge site
http://www.ecst.csuchico.edu/~pieguy/main.html
chip's challenge
http://www.ecst.csuchico.edu/~pieguy/chips/main.php?set=all
Level High Scores for Chip's Challenge
http://www.geocities.com/purpletentacle1977ca/
Chip's Challenge Links
http://www.geocities.com/purpletentacle1977ca/links.html
Chip's Challenge CyberCafe: Level Sets
http://www.geocities.com/snowvale/chipdata.html
Chip's Challenge | Mobile Entertainment Products | Mobile Games | MobileServices | Ringtones | Graphics | MFORMA Group, Inc.
http://www.mforma.com/products/?gameid=050422
Tile World, Windows binary [includes mklynxcc.com]
http://www.muppetlabs.com/~breadbox/pub/software/tworld/tworld-1.2.1-win32.exe
Tile World, Linux source code [includes mklynxcc.c]
http://www.muppetlabs.com/~breadbox/pub/software/tworld/tworld-1.2.1.tar.gz
Tile World
http://www.muppetlabs.com/~breadbox/software/tworld/
Catatonic Porpoise's Chip's Challenge Page
http://www.oceanbase.org/chips/
PrProgramsStudios | Welcome [a Chip's Challenge fan]
http://www.prprogramsstudios.tk/
Welcome to Tile World [see mklynxcc]
http://www.ubergeek.org/~breadbox/software/tworld/README.html

Somewhere in the collection of pages above you may find links to downloada copy of the original Chip's Challenge but it is copyrighted by but nolonger available from Microsoft.

Another game you might find interesting, if you like Chip's Challenge, is Hero's Hearts and its sequels available from Everett Kaser Software.It's similar in operation to Chip's Challenge except that you see theentire map for a puzzle instead of a 9x9 window into it. It wasoriginally written for MS-DOS but it is now availablein a Windows version (and thesequels on the download page (including some user-designed puzzle sets)are only available in Windows versions).

JavaScript Chip's Challenge:

I am also working on implementing some simple Chip'sChallenge-typepuzzles in JavaScript (using Tile World images). There are severaldifferences between my version andthe originals including the fact that it is not 'real time' so adisabled person who can't make moves fast enough isn't prevented fromsolving it.The firstone has just been completed and when the second has been finished thenthe first one will be modified to give the URL for the second one if youwin the game. (Then the second one will be changed to give the URL forthe third one when that one is complete and so on.) The 'differences'file mentioned above has the instructions.

Those who would prefer a timed version with the monsters movingcontinuously may prefer the real-timeadaptation (well, as 'real-time' as you can get considering browserslugishness) of my puzzle by Madhav, AKA 'Keyboard Wielder' (KW)which, on solving it, leads to another Chip's Challenge puzzle byKW.

To create my puzzle (and try other designs), I had to convert a lot ofTile World images from the supplied BMP file into GIF format (includinganimating them.)

A table of most of the Tile-Wold images I haveconverted, leaving out the composite images. (I found iteasier to have effects such as a monster flying over a tile with a key onit if I created composites of some of the transparent GIFs superimposed onFloor tiles.) There are too many images to make all ofthem available (because of space requirements) but a minimum subset of the tiles needed to create your ownpuzzles is available as three zipped files,

  • the non-animated ones,
  • the animated ones and
  • the composite ones (Chip, keys, boots,and monsters over floor).

Oh, and the six-segment digits I used are also available for download, ('0' to '9' and equal-sized blank in threesizes and an HTML page to display them) inone convenient zipped package.

If you want to go to excess in being a Chip's Challenge fan, I havesome Chip's Challenge mouse cursors availablefor download in a zip file. The hot spotsfor the cursors with Chip going East and West is the tip of Chip'soutstretched arm and the hot spot for the cursors with Chip going Northand South is the tip of Chip's arm on your right (Chip's right armwhen he's going North, away from you and his left arm when he's goingSouth, facing you).

Cripple Mr Onion:

Super fill your hard drive mac os. Any fan of Terry Pratchett'sDiscworld series of hilarious fantasy novels is familiar with thethree witches. In the book, Witches Abroad there is a scenewhere some cardsharks get taken to the cleaners by one of the witches,playing a gane called 'Cripple Mr Onion'. If you are too lazy to do yourown laundry, you can try these reconstructed rules for the gameand then you, too, can be taken to the cleaners.

(Information is available on the web for otherDiscworld Gamesas well.)

Some of My Puzzles:

The 'Mindworks' Puzzle (Version 1)

There used to be a store in the Historic Properties of Halifax called'Mindworks' (no relation toAlchemy Mindworks) which sold puzzles,science experimentation kits, and childrens' books about science. I created(for free) the following Move-The-Blocks puzzle for them to use in theiradvertising -- using the words 'Mindworks' and 'Halifax'as significant parts of the puzzle. The store is no longer in businessbut it is a shame to let the puzzle disappear into oblivion.

Instructions:

  1. Print out two copies of the following image, (shown below as ASCII art forlynx users and also as a GIF for graphical browsers) one to use as a templatefor setting up the pieces and one to cut up to make the blocks.
  2. Glue one copy to a sheet of cardboard such as that used with shoe boxesand cut the blocks out along the dividing lines between them. You should havefourteen blocks -- eleven small blocks with 'M', 'D', 'W', 'O', 'S', 'H','A', another 'A', 'X', a 'happy face', and one marked 'empty'; two largerblocks with 'IN' and 'RK', and one triple-sized block with 'LIF' on it.
  3. Lay out the blocks as shown in the 'START' layout -- leaving out the blockmarked 'empty' to leave an empty space. The top row should read 'MINDWORKS' and the bottom row shouls read 'HALIFAX' with thehappy-face to the left of 'HALIFAX' and the empty space to its right.
  4. You can now move one or more blocks per move. A move consists of:
    • Moving a small block up or down to occupy the empty space or
    • Moving one or more blocks to the left or right to occupy the empty space.
  5. Try to rearrange the blocks as is shown in the 'FINISH' template with thehappy-face and the empty space exchanged. It can be done in 76 moves. Canyou beat that score?

Text version for lynx users:

Graphical version:

Ryden life mac os. You can download the same image rotated by 90 degreesto make it easier to print on one page with portrait orientation.

I now have a JavaScript version of the Mindworks Halifax puzzle available foron-line use or downloadable in zipped form for off-line use.

The 'Mindworks' Puzzle (Version 2)

I got to wondering if the puzzle above could be converted to apply toAlchemy Mindworks, which is the zany shareware company that producesgraphic software, screen-saver-creation utilities, and a very funny web site. I tried it and, although the topology was different, it couldbe converted. It takes more moves to solve than the one above.

Dont rage 3 christmas edition! mac os. Using the same rules as above, change this:

Time travel deadmatch mac os. . into this:

It can be solved in 103 moves. Can you beat that? (I don't knowwhether 103 moves is the minimum or not.)

I now have a JavaScript version of the Alchemy Mindworks puzzle available foron-line use or downloadable in zipped form for off-line use.

My 'Halifax', 'Nova Scotia'Puzzle.

If the puzzles above are too hard, follow the same general instructionswith the following image instead -- except the blocks and layout differas this one is based on where I live -- Halifax, Nova Scotia. Thegoal is to exchange the lobster and the empty space. The beginninglayout looks like this:

Text version for lynx users:

Note: The '=' below some of the characters indicatesa Blue character and the '-' below others indicates a Red character.In this puzzle, the placement of the colours is significant. You will needa colour printer to properly print out this puzzle.

Graphical version:

You can download the same image rotated by 90 degreesto make it easier to print on one page with portrait orientation.

New: (November 5,2004) I have now created a computerized version of the NOVASCOTIA puzzle using Just BASIC, a free version ofBASIC from the same people who distribute the shareware Liberty BASIC.To use the game, you need to download and install Just BASIC on your computerand then follow the instructions in my puzzle's HTML documentation,NSPuzDoc.zip [63KB] after also downloadingthe puzzle run-time module and the associated *.bmp files inNSPuzzle.zip [16KB]. [Jan 22, 2005 -- Note tothose who tried downloading it recently and got an error: Try again now.Uploaded files at the Chebucto Community Net used to default toworld-readable but that was changed last year and I still forget at timesto change the file permissions after an upload.] The game isn't finishedyet but is now a working version. ([Dec 21, 2004] Well, it was almostworking. I forgot to disable mouse-clicks at one spot and clicking at thewrong time (while the blocks were moving) gave spurious results. Nowmouse-clicks while the blocks are moving are properly ignored.) To bechanged are:

  1. an UnDo feature to allow backing out of mistaken moveshas yet to be included and
  2. the window used for the game needs to bereduced in size as soon as I no longer need the extra real-estate fordebugging PRINT statements.

New: (May 26,2005):
I have fearlessly but foolishly ventured into the morass of JavaScriptcoding, CSS, Dynamic HTML and Document Object Models and have now createda JavaScript version of my NOVA SCOTIA Puzzle.Sorry, users of old versions of Netscape and Internet Explorer, itrequires Firefox or another browser that supports the W3 DOM (DynamicObject Model) for Dynamic HTML such as the latest versions of Netscape orInternet Explorer. I refuse to use Internet Explorer for anything butgetting Microsoft Security Updates and I don't have Netscape and can'tspare the hard disk space for it. The JavaScript version now has alobster instead of a smiley. When I can find the time to edit allof my images for the puzzle, the smiley will be replaced by a lobster inall of my Nova Scotia versions -- eventually, anyway.

What Is It?

The following is the ingredients list for a product I recentlypurchased. Can you guess what the product is? (Yes, one ingredientis mentioned twice in the ingredients list.) I will post theanswer as soon as I receive one correct guess (or a reasonably closeone).

Ingredients: White Proso Millet, Wheat, Cracked Corn, SunflowerSeed, Corn, Flaked Wheat, Kibbled Corn, Dehydrated Alfalfa Meal, Corn,Corn Distillers Grain with Solubles, Dehulled Soybean Meal, DehydratedCarrots, Wheat Middings, Corn Gluten Feed, Soy Hulls, Bakery Meal,Brewer's Rice, Animal Fat (Preserved with Ethoxyquin), Salt, Dicalciumand Monocalcium Phosphate, Calcium Carbonate, Potassium Sulphate,Magnesium Sulphate, Choline Chloride, Magnesium Oxide, Vitamin ASupplement, Vitamin E Supplement, D-Activated Animal Sterol (Source ofVitamin D3), Niacin, Vitamin B12 Supplement,Riboflavin, d-Calcium Pantothenate, Menadione DimethylpyrimidinolBisulfate (Source of Vitamin K Activity), d-Biotin, Folic Acid, ThiaminMononitrate, Pyridoxine Hydrochloride, Vitamin C, Zinc Sulfate, FerrousSulfate, Manganese Sulfate, Copper Sulfate, Ethylene Diamine Dihydriodide,Cobalt Sulfate, Propionic Acid, Sodium Selenite, Natural and ArtificialColors.

Footnote:
For 'grey', Americans can substitute 'gray'.

A logic puzzle:

https://bluencantadamansionsolar-casinola.peatix.com. Early in 1994 I was a runner-up in a logic puzzle composition contestsponsored by Penny Press® and my name was published in the August 1994issue of their Original Logic Problems. I also received anoffer to buy my puzzle for publication but they required a Social SecurityNumber or equivalent for IRS purposes. As I am in Canada, I wrote that Idon't have a US Social Security Number and am not required by Canadian lawto provide them with my Canadian Social Insurance Number. I never heardback from them (except for the free one-year subscription I also won as arunner-up.)

Since that was eight years ago, I suspect they will not be buying my puzzleat this late date so I present it here for your amusement: Heritage game jam 2020 - paper crusher mac os.

Commander Masters, in charge of the space station 'Deep Space 8' (notas well known as a certain higher-numbered station), has had a busy weeklooking into various accidents, crimes, and other mishaps that seem tooccur all too frequently on her station. This last week has been moreprone to incident than normal due to the temporary influx of severalshiploads of refugees on their way to other planets.

The refugees were from five different planets (Gronge, Hasssth, Kreeoit,Raagth, and Skitskit), had five different body coverings (when undressed)(bare skin, an insect-like exoskeleton, feathers, fur, and scales) andwere of five different colours or colour combinations(black & orange, blue & green,blue & orange, green & yellow, and orange only).In adult form, they also had different numbers and types of limbs; onespecies had 2 legs, 2 wings, and a prehensile tail; another had 4 legs,a prehensile nose, and a prehensile tail; the other three species had only legs and arms but thenumbers varied with the species, 2 legs & 4 arms,4 legs & 2 arms, and 6 legs & 2 arms.

From the descriptions of the mishaps below involving the refugees, determinefor the species of each planet the type of body covering, the colour orcolour combination, and the number and types of limbs.

  1. One mother from Skitskit had to rescue one of her children (which wasstill in its grub stage and hadn't developed an exoskeleton yet) from afeathered being which had mistaken the child for part of its dinner's maincourse. Nursing bruises, the errant diner later protested to the Commander,'Where I come from, anything with orange on it is edible. An oldarmy saying is, 'If you see green, salute it. If you see orange, eat it.'
  2. One being from Hasssth accidentally opened an airlock to space while notwearing a spacesuit. His life was saved by the quick action of the memberof another species who immediately hit the emergency override pressurizingswitch with one of her furry limbs. 'I was looking for the men's washroom.'was his excuse for the incident.
  3. A scaly and a furry being got into a fight over which had the nicestblue trim on his body. The fur-bearer broke his nose punching the otherin the ribs. Both were arrested for public intoxication and disturbingthe peace.
  4. A four-legged being with black spots insulted a Hasssthian and aKreeoitian by claiming that the colour green is the colour of spoiled foodand by suggesting that the other two should be disinfected. Don't worry;the doctors in the infirmary say that he will recover -- eventually.
  5. A member of one species ended up in the infirmary with some of her orangescales abraded off when her tail was stepped on in the crowded mall area.The Commander talked her out of suing the station.
  6. One Raagthian found out that having more legs didn't necessarily meanthat one runs faster after he snatched the purse from a Skitskitian. TheSkitskitian caught up with him and beat him over the head with her(otherwise superfluous) umbrella. 'What's this galaxy coming to? Youcan't even trust a little old lady these days!' he said as he was ledoff to the brig.

You should now have enough information to fill in the following chart:

Webmaster: Norman De Forest,
Email me if you havecomments on my site.

VersionMAJ

concaterpillar

1.52013-01-15DownloadDoc
Concaterpillar is a hierarchical likelihood-ratio test for phylogenetic congruence.

Remarque If you use Concaterpillar for a publication please cite: Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008 Feb; 57(1): 104-15.
Run Unix # concaterpillar.pyRun Web #
VersionMAJ

consel

0.22012-08-23DownloadDoc
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique. This newly developed method gives less biased results than the conventional methods.

Remarque
Run Unix #Run Web #
VersionMAJ

CopyRighter

0.462015-12-21DownloadDoc
Parses microbial profiles and, because gene copy number (GCN) estimates arepre-computed for all taxa in the reference taxonomy, rapidly corrects GCNbias. The CopyRighter bioinformatic tools permits rapid correction of GCN inmicrobial surveys, resulting in improved estimates of microbial abundance,alpha and beta diversity.

Remarque
Run Unix # copyrighter -i [optional arguments]Run Web #
VersionMAJ

indel-Seq-Gen

2.1.032012-08-24DownloadDoc
indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the 'true' multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods. iSG utilizes a highly modified version of the substitution engine from Seq-Gen v1.3.2.

Remarque
Run Unix # indel-seq-gen [-bdefghilmnoqsuwz] < [tree_file] (indel-seq-gen -h)Run Web #
VersionMAJ

modelgenerator

0.852011-03-15DownloadDoc
ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

Remarque
Run Unix # modelgeneratorRun Web #
VersionMAJ

modeltest

3.72006-11-20DownloadDoc
Modeltest est un programme qui évalue différents tests de rapport de vraisemblance de modèles d'évolution dans le but de choisir le modèle le plus approprié aux données.

Remarque
Run Unix # modeltestRun Web #
VersionMAJ

MrBayes

3.2.52015-10-20DownloadDoc
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Remarque
Run Unix # mbRun Web #
VersionMAJ

njplot

20092013-08-27DownloadDoc
NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Remarque
Run Unix # njplotRun Web #
VersionMAJ

paml

4.92015-03-30DownloadDoc
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

Remarque
Run Unix # #baseml (basemlg codeml pamp evolver yn00 chi2)Run Web #
VersionMAJ

phast

1.32013-07-23DownloadDoc
PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Remarque
Run Unix # phastRun Web #
VersionMAJ

phylip-3.69

3.692013-02-21DownloadDoc
PHYLIP is a free package of programs for inferring phylogenies.

Remarque
Run Unix # dnaml Run Web #http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
VersionMAJ

phylobayes

3.3f2013-08-22DownloadDoc

Puzzlerun Mac Os Catalina

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction and molecular dating using protein and nucleic acid alignments. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the use of nonparametric methods for modelling site-specific features of sequence evolution.

Remarque
Run Unix #Run Web #
VersionMAJ

PhyML

3.12014-08-06DownloadDoc
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used (>1,250 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued. We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task. It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.

Remarque
Run Unix # phymlRun Web #
VersionMAJ

ProtTest

3.02011-08-03DownloadDoc
PROTTEST3 is a high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences. This java program uses the Phyml program (for maximum likelihood calculations and optimization of parameters) and the PAL library for handling trees, and the ALTER library for reading aligment formats. Empirical models included are as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb/HIVw and FLU, plus +I:invariable sites, +G: rate heterogeneity among sites and +F: observed amino acid frequencies. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc, BIC and DT) to find which of the candidate models best fits the data at hand. It also implements the calculation of model-averged phylogenies.

Remarque Citation: Darriba D, Taboada GL, Doallo R, Posada D. In press. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics.
Run Unix # runProtTestHPC ou runXProtTestHPCRun Web #
VersionMAJ

QuickTree

1.12006-02-21DownloadDoc
QuickTree is a program for the rapid reconstruction of phylogenies by the Neighbor-Joining method. For details, see the article published in the journal 'Bioinformatics' (18:1546-1547).

Remarque
Run Unix # quicktreeRun Web #
VersionMAJ

raxml

7.3.02013-04-11DownloadDoc
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel MaximumLikelihood [1] based inference of large phylogenetic trees. It has originally been derived from fastDNAmlwhich in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP [2] package.

Remarque If you use RAxML please always cite the following paper: Alexandros Stamatakis : 'RAxML-VI-HPC:Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models', Bioinformatics22(21):2688–2690, 2006 [4].
Run Unix # raxmlHPC -h ou raxmlHPC-MPI -hRun Web #
VersionMAJ

seq-gen

1.3.32012-08-24DownloadDoc
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

Remarque
Run Unix # seq-genRun Web #
VersionMAJ

splitsTree

4.13.12014-06-23DownloadDoc
SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

Puzzlerun Mac Os X


Remarque
Run Unix # SplitsTreeRun Web #
VersionMAJ

tree-puzzle

5.22012-08-22DownloadDoc

Puzzlerun Mac Os Download

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, one and two-sided Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters (except for GTR) can be inferred from the data set.

Puzzlerun Mac Os Update

Mac

Remarque
Run Unix # puzzleRun Web #




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