As people can see from the dates on the most recent updates of these Phylogeny Programs pages, I have not had time to keep them up-to-date since 2012. I have now retired, which gives me more time to do research and to support online resources. So I have hopes of resuming updates, fixing links, and catching up with the field of phylogenetic inference. In the meantime, I may not be able to devote time to searching for new programs, so their authors are begged to (please!) use the submission form instead. That form will be found at the 'Submitting' link below.
If you are upset that your program is not included, but it's too much trouble for you to fill out the submission form, then I will not listen to you. If anyone else wants to help with this, let me know. Here are 392 phylogeny packages and 54, (almost) all that I know about. It is an attempt to be completely comprehensive.
I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly monthly.
Is a 'waiting list' of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from. The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free.
I have listed as free those that I knew were free; for the others you have to ask their distributor. Usually when I say that a program is downloadable from a web site, this means that it is available free. Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses. If you discover any inaccuracies, or feel that I have left any important programs or facts out, or if links do not work properly, please e-mail me at: ( joe (at) gs.washington.edu).
You can also use the submission form to submit new entries.
BioEdit is a very popular sequence alignment editor. It was written by Tom Hall and it was made only for Windows. This tutorial will show you how to install BioEdit on a Mac without the use of Parallels Desktop or other virtual desktop software running Windows in the background. You’ll first need to install Wine. To install Wine on your Mac, you’ll need an Intel Mac and should follow (check the comments below. Some users have had success while others had some problems).
Follow his guide until you finish Part 3 Install Wine using MacPorts. Then return to this page. Install BioEdit using Wine To install a BioEdit program, first download the installer file. It should end with.exe. Save the BioEdit installer file in your user directory (it should show up on the Places in your Finder, below your Desktop icon, and shows up as a little house icon). Open Terminal and run the installer through Wine by using this command: $ wine setup.exe XQuartz will open (if it isn’t already), and soon you will the installer. Click through it to install the program.
Install Winetricks To make BioEdit work, you’ll have to do some additional installations. In the Terminal window, type: $ sudo port install winetricks $ sh winetricks mdac27 The Terminal will open the webpage in your browser. Download the software from the website and put it in /Users/YOURNAME/Library/Caches/winetricks/mdac27 Then on the Terminal window type again: $ sh winetricks mdac27 Run BioEdit Now you are ready to launch BioEdit. To run BioEdit, type in Terminal: $ cd /.wine/drivec/BioEdit $ wine BioEdit.exe Make an short cut for launching BioEdit (optional) It would be nicer not having to go to the Terminal everytime you want to use BioEdit. You can make a icon that you can put on your dock in order to launch BioEdit quickly.
Go to your Spotlight search at the top right corner and type “AppleScript Editor”. Once the program opens, in the big blank space, copy and paste the following: tell application 'Terminal' do script '/opt/local/bin/wine /.wine/drivec/BioEdit/BioEdit.exe' end tell Next, press the Compile button at the top of the window. The text should become colored. Try pressing the Run button to run your script and it should open BioEdit successfully. Save your script. You can give it whatever name you’d like, but be sure to select File Format: Application in the save options, and leave Startup Screen unchecked. Open up the Finder, go to where you saved your script/app, and drag that file to your Dock.
It should stay there, just like a real application. Now you can click it to launch BioEdit quickly without having to type in the Terminal. Diana I was really hoping I would get this to work, but I’m running Mac OS X 10.7 (Lion) and it doesn’t seem to work.
I get hung up at step 2:install wine using MacPorts. I get the following warnings – any suggestions? Warning: The Command Line Tools for Xcode don’t appear to be installed; most ports will likely fail to build. Warning: See for more information. — Computing dependencies for wineError: Unable to execute port: can’t read “build.cmd”: Failed to locate ‘make’ in path: ‘/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin’ or at its MacPorts configuration time location, did you move it? To report a bug, see Thanks! Plinio Trabasso Hi, I’ve got the same problem reported by Diana.
During Step 2, I got the message below: Warning: The Command Line Tools for Xcode don’t appear to be installed; most ports will likely fail to build. Warning: See for more information. — Computing dependencies for wineError: Unable to execute port: can’t read “build.cmd”: Failed to locate ‘make’ in path: ‘/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin’ or at its MacPorts configuration time location, did you move it? To report a bug, see I’m using MacOS Lion (10.7), running appropriate versions (i.e, MacOS 10.7) of Apple Xcode, Java Development Package and MacPorts.
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Do you have any suggestion? Thanks Plinio. Hi there, I completed till part 4 without any problems but I am stuck in part 5 i.e.
Run BioEdit section. When I typed cd /.wine/drivec/BioEdit it says that “No such file or directory” I am wondering to where I should change my working directory. It didn’t find any BioEdit packages in my system Actually, it’s in the downloaded folder the whole bioedit packages and I didn’t change the location of the downloaded packages. So, to where I should change my working directory to run the BioEdit?
Nathan McNulty Seems that I spoke too soon, sort of — one of the features of BioEdit I value most highly (i.e., pairwise alignments while allowing ends to slide) appears to be broken now. Attempting such an alignment on 10.8.2 generates the following error, which I didn’t get before: “External exception EEFFACE.” A little Googling around suggests this may be the result of attempting to read/write beyond the bounds of a std::vector in C Builder. Runtime exceptions like this go far beyond my debugging abilities.
Is anyone else with a 10.8.2 installation able to perform pairwise alignments while allowing ends to slide? I’ve never been able to find other software that allows me to do this, so I’m keen to get this working again. Nathan McNulty Moderator, feel free to remove this comment and my previous one about the EEFFACE errors I’ve been getting. While the error is legitimate for the first sequences I tested, it seems to somehow be specific to sequences that I’ve imported. If I create two new sequences from scratch within BioEdit and attempt to align them, things work fine.
I’m guessing there must be some pernicious formatting error with my inputs that was causing the problems — it probably has nothing to do with the installation per se. Omer Hi, I have a iMac OS X 10.8.2 I colud do up to part 3. I wrote ‘sudo xcodebuild -license’ and than read and wrote ‘agree’ Terminal have responded ‘You can view the license agreements in Xcode’s About Box, or at /Applications/Xcode.app/Contents/Resources/English.lproj/License.rtf’ I have closed and reopened terminal window and than I have entered command (sudo port install wine) terminal responded: Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘sudo’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘xcodebuild’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘if’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘‘, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘`sysctl’, ignored. Track4win keygen for mac. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘hw.cpu64bitcapable`’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘1’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘;’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘then’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘echo’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘”+universal”‘, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘ ’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘sudo’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘tee’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘/opt/local/etc/macports/variants.conf;’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘else’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘echo’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘”not’, ignored.
Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ’64bit’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘capable”;’, ignored. Warning: /opt/local/etc/macports/variants.conf specifies invalid variant syntax ‘fi’, ignored. Error: Port wine not found I did not understand help me? Kim Hi I am stuck on here. Anybody can help me? I am using mountain lion.
MacBook-Pro: apple$ sh winetricks mdac27 Executing wdocall mdac27 Executing loadmdac27 Using native,builtin override for following DLLs: odbc32 odbccp32 oledb32 Executing winetricksearlywine regedit C: windows Temp mdac27 override-dll.reg Setting Windows version to nt40 Executing winetricksearlywine regedit C: windows Temp mdac27 set-winver.reg Executing wine /Users/apple/Library/Caches/winetricks/mdac27/mdactyp.exe Application tried to create a window, but no driver could be loaded. Make sure that your X server is running and that $DISPLAY is set correctly. Err:systray:initializesystray Could not create tray window Application tried to create a window, but no driver could be loaded. Make sure that your X server is running and that $DISPLAY is set correctly.
—————————————————— Note: command ‘wine /Users/apple/Library/Caches/winetricks/mdac27/mdactyp.exe’ returned status 43. Libby So after a few days of errors and google, I have managed to successfully complete the install. First, the homebrew installation of Wine does not work, others have had the same problem with being stuck in the installer. Uninstall of wine was partially successful the.wine directory remained and needed to be removed manually, the uninstall of homebrew had some scary comments that the provided script could damage the system. Instead I removed everything from /usr/local that homebrew had installed there. I then reinstalled wine via macports the alternate page on the site with the homebrew instructions. Then installed winetricks.
I then removed the.wine directory as it was returning an error when trying to install the mdac27. Installed mdac27 with winetricks. The ran the setup.exe for BioEdit. I found I needed to do the mdac27 installation first to get the installer to run. Finally I could run BioEdit. I did get a Dynamic session lookup error saying “launchd did not provide a socket path, verify that org.freedesktop.dbus-session.plist is loaded!” which didn’t seem to affect BioEdit loading, but I corrected it as well. Hope it works well now.
So far I have been able to open old alignments and manipulate as previously. Libby I am having the same issue as Ivan, also Macbook Pro OS X 10.8.4. Installed Wine via Homebrew as per the recommendations on the linked page, and installed winetricks mdac27 using the brew command instead of port. When executing wine setup.exe from the home directory the first few windows appear initializing installer, etc.
Then the first msi window the blue and white one appears and upon selecting next the system stalls. The same fixme: error as above appears often before clicking next. Running WINEDEBUG shows where it stalls and it seems hung up on drawing the next window which would have the license information. Much googling gave no results except those that said a fixme shouldn’t be a catastrophic error. Any help would be appreciated. Phylogeneticgeek Thank you everyone for coming back to comment whether you were successful or you had problems but eventually figured out the solution. This is what science/life is all about right?
Share what we know so it may help someone else. This is exactly why I started this post in the first place almost 3 years ago.
Unfortunately I have been so incredibly busy with my doctoral studies that I no longer have the time to properly manage this page at a satisfactory level. Hopefully new users will read what you’ve all contributed in the comments section if they are running into problems.
Again, thank you so much for your contributions. Phylogeneticgeek I tried what Sam suggested and here’s some very rough step by step instructions. Download WineBottler here.
Also make sure you have XQuartz installed. Open the WineBottlerCombo1.4.1.6.dmg file and drag Wine and WineBottler apps to your Applications folder. Open WineBottler app 4. Click on the Advanced Tab. Under “Program to Install”, click “Select file” and then pick the setup.exe for BioEdit.
Go to the BioEdit site if you don’t have it. Leave the button on “This is an installer, execute it.” 6. Where it says “Winetricks”, scroll down until you see “mdac28” and click on the box to checkmark it. Where it says “Bundle”, click to check the box for “include wine binaries” 7. On the bottom of the page, click on Install.
Some windows will pop up, just click to accept licenses/etc just as you would install these programs under Windows. Once it’s finished, it will create the.app. I called it BioEdit.app. Click BioEdit.app to run it. That seemed to have worked for me. Bandara I canot install winetricks.
Once “sudo port install winetricks” command run following massage was displayed. Help Admins-MacBook-Pro: admin$ wine setup.exe err:winediag:SECUR32initNTLMSP ntlmauth was not found or is outdated. Make sure that ntlmauth = 3.0.25 is in your path. Usually, you can find it in the winbind package of your distribution.
Fixme:iphlpapi:NotifyAddrChange (Handle 0x10ef550, overlapped 0x10ef55c): stub wine: configuration in ‘/Users/admin/.wine’ has been updated. Fixme:storage:createstoragefile Storage share mode not implemented. Admins-MacBook-Pro: admin$ sudo port install winetricks Password: Warning: port definitions are more than two weeks old, consider using selfupdate — Extracting zlib Error: org.macports.extract for port zlib returned: command execution failed Please see the log file for port zlib for details: /opt/local/var/macports/logs/optlocalvarmacportssourcesrsync.macports.orgreleasetarballsportsarchiverszlib/zlib/main.log Error: Problem while installing zlib Error: Unable to execute port: upgrade openssl failed Admins-MacBook-Pro: admin$. Thank you very much!!!I successfully installed BioEdit following your tutorial, although having lots of error and trial. I am new to Mac, so had lots of problem and would say that its not easy to install. But few things to add that: 1. Install Wine using MacPorts, another alternative (as from Homebrew it took hardly 10 minutes to install and was not complete).
I install Winetricks before BioEdit. After installing Winetricks at command (sh winetricks mdac27), I could not find Library in my User directory, then I learned it is hidden by default in Mac OS x10.8 or newer version. Which I Open by giving command in terminal (chflags nohidden /Library/), it will permanently reveal your Library in user directory, but if you want to hide it again for safety purpose, give the command (chflags hidden /Library/). After that, as written Xquartz will open, I don’t why, it did not happen in my case.
But I proceed further. While installing BioEdit, when I gave command $ wine setup.exe, it showed some error (wine: cannot find L”C: windows system32 install.exe”). Instead of pasting whole folder there, I copied all files of BioEdit zip folder one by one in user directory and tried again, which worked.
Then I followed the instruction and it worked without any error. I am highly Thankful to all of you guys, your feedback really helped me a lot to bring BioEdit in my life again. It would be helpful if someone shares about how to install MEGA programme on Mac. Just to add information that I installed BioEdit 5.09 version on MacBook Pro OS x 10.8.5. Whenever I open BioEdit, terminal also open and says: /opt/local/bin/wine /.wine/drivec/BioEdit/BioEdit.exe Farzanas-MacBook-Pro: fsabir$ /opt/local/bin/wine /.wine/drivec/BioEdit/BioEdit.exe Dynamic session lookup supported but failed: launchd did not provide a socket path, verify that org.freedesktop.dbus-session.plist is loaded! Err:ntdll:RtlpWaitForCriticalSection section 0x7bc8fc74 “loader.c: loadersection” wait timed out in thread 001c, blocked by 001d, retrying (60 sec) and then it opens the BioEdit window. I was wondering if it is the normal way of opening BioEdit or am I missing something, although after opening BioEdit works perfect.
Meg Can someone help me? I’m a computer programming N00b and I’ve managed to successfully follow the steps up until Wine Tricks. I type in the commands as stated “sudo port install winetricks” but after entering my password I am told “sudo: port: command not found” Any suggestions? I also get this message when I run brew doctor: (not sure if it means anything) Warning: Homebrew’s sbin was not found in your PATH but you have installed formulae that put executables in /usr/local/sbin.
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Consider setting the PATH for example like so echo export PATH=’/usr/local/sbin:$PATH’ /.bashprofile THANKS!!!! Reynaldo hello, my name is Reynaldo, I am trying to install Bioedit in mac OS X 10.9.4, but I have a hurt time with this. However I get all the step 1, 2 and 3 in installling wine on mac and then I follow thw step on I get the instal bioedit using wine but when I try to install winetrick, I have this problem: MacBook-Pro-de-MACARENA:BioEdit macarenadelpilarbarrajimenez$ wine setup.exe fixme:storage:createstoragefile Storage share mode not implemented. Fixme:ntdll:findregtzinfo Can’t find matching timezone information in the registry for bias 240, std (d/m/y):, dlt (d/m/y): 7/09/2014 MacBook-Pro-de-MACARENA:BioEdit macarenadelpilarbarrajimenez$ sudo port install winetricks Password: sudo: port: command not found there are someone who guideme from this step? Look at rural real-estate not for the purpose it is, but for which it could become. They will provide appropriate advice on the form of facility to rent from them and whether can suit your neexs or not.
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I am using OS X Yosemite 10.10.3. I tried everything in detail. But the Homebrew gave me some trouble. When I ran the Brew doctor, I got warning ‘some un-brewed.pc apps were detected’. Also got license errors but this was solved the command ‘$ sudo xcode build -license’. So, I could manage to install wine via Homebrew using the Terminal, and therefore did not make to install the Winetricks and theBioedit.exe with Homebrew via wines. The separate (without using the command line) downloads and installations of the Xcode, the Java, the XQuartz, and the wine+the winebottler the went successfully.
Download Bioedit Software
Finally I tried the wineskin application, which I had previously downloaded from the. By launching the wineskin, you get a window with “install Software”, “Set screen Options” “Advanced” “Quit”. I clicked on the “Advancedconfigurations”, I located and installed a wrapper called “MyCoolWrapper”. By going to “Advanced””Tool””Winetricks””dlls” I selected both the ”mdac27” +”mdac28”. And used the “run” button at the middle right part of the dialogue box. I went back to configurations and browse to locate the bioedit.exe and installed the software successfully. I went back to the configurations and this time round I did the testrun using the button bottom right hand side.
And with success the bioedit could open as it does normally in windows. The Goal achieved! Thank you guys for sharing.
Evans Rono Hello the good people, After some day and a night of technicalities, Wineskin finally worked for me. I am using OS X Yosemite 10.10.3.
I tried everything in detail. But the Homebrew gave me some trouble. When I ran the Brew doctor, I got warning ‘some un-brewed.pc apps were detected’. Also got license errors but this was solved the command ‘$ sudo xcode build -license’.
So, I could manage to install wine via Homebrew using the Terminal, and therefore did not make to install the Winetricks and theBioedit.exe with Homebrew via wines. The separate (without using the command line) downloads and installations of the Xcode, the Java, the XQuartz, and the wine+the winebottler the went successfully. Finally I tried the wineskin application, which I had previously downloaded from the. By launching the wineskin, you get a window with “install Software”, “Set screen Options” “Advanced” “Quit”. I clicked on the “Advancedconfigurations”, I located and installed a wrapper called “MyCoolWrapper”. By going to “Advanced””Tool””Winetricks””dlls” I selected both the ”mdac27” +”mdac28”.
Bioedit Similar Mac
And used the “run” button at the middle right part of the dialogue box. I went to “Install software” button and located the Bioedit.exe while specifying it as a copy of the original Bioedit. It installed successfully. This step must be done for all other windows softwares.
I then went back to configurations to locate the bioedit.exe file installed and run the software successfully. For this, clicked the “testrun” button at bottom right hand side. And with success the bioedit could open as it does normally in windows. The Goal achieved!
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Sam Lewis Thanks very much for this guide, it’s extremely helpful! I encountered a couple of minor problems when installing on El Capitan 10.11.3, so am posting the adjustments here in case anyone else finds them helpful. Follow the instructions in the article up to “Install WineTricks”, then type: # install winetricks sudo brew install winetricks # install additional packages sh winetricks mdac27 # launch BioEdit to check installation success cd /.wine/drivec/BioEdit wine BioEdit.exe Then follow the instructions to make a shortcut for launching Bioedit, but change the content of the script to: tell application “Terminal” do script “/usr/local/Cellar/wine/1.8/bin/wine /.wine/drivec/BioEdit/BioEdit.exe” end tell. Rexmilleruser Hi, I did once install this successfully – but since changing laptop it has failed repeatedly. Kevin G I am having a combination of issues similar Ana Paula and Alexandre. When I try to run ‘sh winetricks mdac27’, I receive the error: This package does not work on a 64-bit installation.
You must use a prefix made with WINEARCH=win32. I created 32-bit Wine prefix using some of the tricks found here When I try to run ‘sh winetricks mdac27’ using the 32-bit prefix, I get the following error: WINEARCH=win32 WINEPREFIX=/Users/kevingallagher/.wine32 wine sh winetricks mdac27 wine: cannot find L”C: windows system32 sh.exe Anybody make it through these issues? Kevin G In case anyone else has this issue, I found a solution based on this article: (worked for OS X Sierra, even tho this solution was meant for ubuntu) Specifically, I followed the instructions in the comment by Cristiana Nicolae: “First I deleted the Wine folder with this command: rm -r /.wine If it tells you that directory is not empty just add the -f (force) flag. Note that this will remove any windows applications installed in this prefix!
Your command should look something like this: rm -r -f /.wine And then create a 32 bit prefix with this command: WINEARCH=win32 WINEPREFIX=/.wine wine wineboot “. Tupe I have some problems installing bioedit. Anybody has encountered this and have a solution.
This inexpensive monitor from LG has the company's excellent IPS panel, as a well as a very fast 5-millisecond response time. With a refresh rate of 60Hz, excellent viewing angles, and a designated gaming mode, this is a solid all-around monitor for most people. It doesn't offer much regarding inputs (HDMI and DisplayPort only), but it'll do in a pinch. Monitors can be expensive, but if you're on a tight budget like me, the 's a perfect way to get the 4K resolution you want and save a few bucks. Regardless of what you pick, and of these monitors will make a great addition to any workspace. This post may contain affiliate links. See our for more details.
No, the software is not available for Mac OSX. I've checked and it appears that the software isn't even supported and maintained anymore. It can be considered as being discontinued even if there are downloads available. This also means there won't be a version for Mac OSX in the future as well. The only way to run the software is by installing Windows through Bootcamp or virtualize it using Parallels Desktop, or you could try Wine Bottler, the famous app that can run Windows software without having Windows installed.
Download Wine Bottler:. Download software.
Documentation links admin & aux services Equivalent Applications for GCG programs GCG on the SACS system will be retired in Fall 2010. Most of the GCG programs are available in. This table lists the EMBOSS equivalent for each GCG program, or where applicable, an alternative program that is available on the SACS System. GCG program EMBOSS program Description/Comments Assemble Construct new sequences from pieces of existing sequences; merger only accepts 2 sequences while assemble and union accept several. BackTranslate Backtranslate protein - nucleotide sequence.
Backtranambig backtranslates to ambiguous codons. BestFit Bestfit uses the Smith-Waterman algorithm to find the best local alignment between 2 sequences. Water uses Smith-Waterman, matcher uses Pearson's lalign algorithm. Blast Psiblast NCBI homology search between query and database Breakup Splits a sequence into (overlapping) smaller sequences Chopup - Helps to convert a non-GCG sequence format Not needed in EMBOSS because it reads most sequence formats without conversion CodonFrequency CodonFrequency -tabulates codon usage. Compseq - counts composition of dimer/trimer in sequence. Chips - calculates codon usage stats cusp - creates a codon usage table.
CodonPreference Recognize protein coding sequences CoilScan Predicts coiled-coil regions Compare + DotPlot + 2-sequence comparison. Dotpath does a non-overlapping wordmatch dotplot. Composition Sequence composition compresstext - Removes extra whitespace in text files. Can be done via Unix shell script. Comptable - Creates a scoring matrix consensus Creates a consensus sequence or matrices/profiles from multiple alignments correspond Codon usage table comparison corrupt Randomly mutate sequence dataset Creates searchable sequence database.
GCG's Dataset requires sequences in GCG format, whereas dbiflat, dbiblast, dbigcg will take most formats between them. Detab - Replaces tabs with spaces in sequence files. Can be performed by Unix shell command. Distances - Calculates pairwise evolutionary distances between aligned sequences. The Phylip package can do this.
Diverge - Estimates pairwise substitutions per site between 2 or more coding sequences. The Phylip package can do this. Dotplot 2-sequence comparison extractpeptide ExtractPeptide takes the output of Map and can write one or more of the reading-frame translations. Transeq translates one or more of the frames or specific regions directly from an input nucleotide sequence. FastA FastX Tfasta TfastX - Pearson's homology-search programs. Fetch Pull one or more sequences out of the databases.
Seqret/seqretsplit can save output in various sequence formats. Figure - Generates plots from other GCG programs. The equivalent EMBOSS programs usually generate plots (e.g. Findpatterns searches for patterns in a sequence or database fingerprint - Finds the products of T1 ribonuclease digestion. Fitconsensus - Use after Consensus to find the best fits.
Framealign - Finds best local alignment including frame shifts between a protein and nucleotide sequence. Frames Show open reading frames. Plotorf does this graphically framesearch - Homology searches including frameshifts between protein and nucleotide sequences fromembl fromfasta fromgenbank fromig frompir fromstaden fromtrace - Converts from various formats to GCG sequence format. Unnecessary in EMBOSS because it can accept most sequence formats, but seqret can convert between formats if desired. Gap Needleman-Wunsch algorithm to compare 2 sequences. Stretcher uses the Myers-Miller algorithm which is more memory-efficient. For sequences larger than 10kb, I would suggest you to use 'stretcher' program in EMBOSS which is also a global alignment program.
If one of your sequence is genomic and you are trying to align an est sequence to it, you may want to consider the 'est2genome' program. On the other hand, water-matcher-supermatcher are local alignment programs for small, medium, and large sequences, respectively. Gapshow Graphical representation of similarity of 2 sequences. GCGtoBlast - Makes a Blast database. Use NCBI's 'formatdb' instead. GelAssemble GelDisassemble GelEnter GelMerge GelStart GelView Parts of GCG's gel assembly suite.
GetSeq Type in a new sequence GrowTree - Creates phylogenetic tree. Can use Phylip or Clustal instead. HelicalWheel Plots peptide sequence as helical wheel to help recognize amphiphilic regions. HmmerAlign HmmerBuild HmmerCalibrate HmmerEmit HmmerFetch HmmerIndex HmmerPfam HmmerSearch - Sean Eddy's HMMER package.
HTHScan Finds HTH motifs in protein sequences. IsoElectric Calculates isoelectric pt of protein. Lineup - Edits multiple sequence alignments ListFile - for printing. Can use Unix pcprint command instead. Lookup - Versatile program for finding sequences in a database. In emboss can search for accession numbers, but GCG's lookup is much more sophisticated. Map Mapplot Mapsort finds restriction enzyme cleavage sites.
GCG & EMBOSS may display different isoschizomers of the same enzyme, but the results are equivalent. The EMBOSS remap program may not display a few of the available isoschizomers. MeltTemp Computes melting temperature of oligos MEME - Finds conserved motifs in a group of unaligned sequences. MFold - Predicts nucleotide secondary structure.
GCG's version is an old version of Zuker's MFOLD. Moment, Makes a contour plot of the helical hydrophobic moment of a peptide sequence hmoment prints the text output of the calculation.
Motifs Finds common Prosite motifs in a sequence. Use '-full' tag to display abstract information when using EMBOSS patmatmotifs. Note that both these programs will only find Prosite 'Patterns' (e.g. CAMP Phosphorylation Site), and not Prosite 'Matrices' (e.g. Use to find all known domains and functional sites. (patmatmotifs can accept file containing multiple sequences or patterns.
Meme + Motifsearch + Search a sequence or database with a matrix or profile. Names provides some info about sequence specifications.
NetBlast Netfetch - remote access to NCBI's Blast. NoOverlap Finds differences between 2 sequences. NoOverlap can work with a group of sequences. OldDistances - Makes a table of the pairwise similarities within a group of sequences. Onecase - converts sequence into lower or upper case.
Can be performed by Unix shell command. Overlap - Compares 2 sets of sequences using Wilbur-Lipman algorithm. Paupdisplay + Paupsearch - PAUP Phylogenetic Analysis./td Pepdata Translates in all 6 reading frames. Sixpack displays the DNA sequence with 6-frame translations and orfs. Pepplot Pepplot plots protein 2ndary structure and hydrophobicity.
Bioedit Alternative Mac
Pepinfo plots hydrophobicity, and garnier does protein 2ndary structure prediction. Peptidemap Enzyme/reagent cleavage map of a protein. Peptidesort GCG peptidesort sorts fragments from an enzyme/reagent cleavage of one or more proteins according to position, mol. Wt., and HPLC retention. EMBOSS digest only processes one reagent cleavage at a time. EMBOSS pepstats can be used to determine the composition of the fragments afterwards.
The EMBOSS programs do not provide the elution times from HPLC. If you need this data, try the which has an option for HPLC Indices.
Peptidestructure Plotstructure Secondary structure prediction. Garnier does not include Jameson-Wolf antigenic indexing. Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.
Pepwindow displays Kyte-Doolittle protein hydropathy. Pepwindowall produces a set of superimposed Kyte & Doolittle hydropathy plots from an aligned set of protein sequences. Pileup Multiple sequence alignment. Emma is an interface to ClustalW. PlasmidMap Plot DNA constructs.
PlotFold - Plots MFold output. PlotSimilarity Graphical representation of the similarity along a set of aligned sequences. Pretty prettybox Calculates consensus sequence from a multiple sequence alignment, and displays them prettily. Prime Selects oligonucleotide primers. Profilegap Profilemake Creates matrices/profiles from multiple alignments. Gapped alignment for profiles and sequences.
Evaluates individual primers to determine their compatibility for use as PCR primer pairs. Profilescan Searches sequences or db for protein motifs. Profilescan uses Gribskov method. Profilesearch Scans a sequence or database with a matrix or profile. Profilesegments - Alignments for results of Profilesearch Publish Makes publication-quality displays of sequences. Reformat GCG requires input sequences to be in GCG format, hence other formats need to be converted with 'reformat'. Emboss programs accept most sequence formats, so conversion is rarely required, but 'seqret' can be used to convert between formats if desired.
Repeat Finds tandem repeats in sequences. The equivalent group of Emboss programs will also look for inverted or palindromic repeats. Replace Replaces characters in a text file.
Degapseq is specific for replacing gap characters. Can be performed with Unix shell utilities like sed, awk or tr. Reverse Reverse/complement a sequence. Sample Extract regions from a sequence.
Seg Masks off low-complexity regions from a sequence. Seqed, Sequence editor. EMBOSS has several tools for specific editing tasks. Or use a text editor (not word processor!). Try the for editing multiple sequence alignments. Other alternatives are (Windows only) and (Mac, Windows, Unix). SeqLab - X-windows interface to GCG.
Setkeys - Redefines keyboard keys, mainly used for GCG's gel assembly programs. Shiftover - Moves text by column. Use the nedit editor instead. Shuffle Shuffles a sequence. Simplify - Reduce the number of symbols in a sequence.
Spew - Sends a sequence from a remote computer to your desktop. Use one of the File transfer mechanisms instead. SPScan Predicts signal peptides in protein sequences. Ssearch - Part of Pearson's Fasta package.
StatPlot - Plotting program. StemLoop Finds inverted repeats. Stringsearch Finds text phrases in sequence or database. Terminator - searches for prokaryotic factor-independent RNA polymerase terminators according to the method of Brendel and Trifonov. Testcode Plots 3rd-position variability as an indicator of potential coding regions. ToFastA ToIG ToPIR ToStaden Emboss accepts most sequence formats, therefore format conversion is rarely required.
Seqret can be used to convert between formats if desired. Translate Translates nucleotide - Protein sequences Transmem - predicts transmembrane helices.
Window + Statplot Residue/base frequency table or plot. Wordsearch Segments - Homology search using Wilbur/Lipman algorithm. Segments displays the result. Xnu - Masks tandem repeats for future Blast search. Reads ABI file and displays trace - Finds antigenic sites in proteins - Bending and curvature plot in B-DNA - Calculates the twisting in a B-DNA sequence - CAI codon adaptation index, to measure synonymous codon usage bias. Create a chaos game representation plot for a sequence - Protein charge plot. Reports STOP codons and ORF statistics of a protein - Extract CDS, mRNA and translations from feature tables - Plots and reports CpG-rich regions.
Seqed Removes a specified section from a sequence. Seqed is interactive, cutseq is command-line. Seqed Alter name/description of sequence. Findpatterns Regular expression search of a sequence. Findpatterns is an approximate equivalent. interface to ClustalW program. Protein identification by Mass spectrometry.
Finds PEST motifs as potential proteolytic cleavage sites - Align EST and genomic DNA sequences. Extract features from a sequence. Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot - Protein pattern search after translation - Calculates the fractional GC content of nucleic acid sequences - Plots isochores in large DNA sequences - Writes a list file of the logical OR of two sets of sequences - Create random nucleotide and protein sequences - Finds MAR/SAR sites in nucleic sequences - Mask off features of a sequence.
Shows molwts that match across a set of files - Filter noisy molwts from mass spec output - remove carriage return from a ASCII files. Can be performed by Unix utilities like 'tr'. Reformat Pulls one sequence out of a multiple set.
Reformat will pull a sequence out of an MSF or RSF file. Finds protein sequence regions with a biased composition - Displays all-against-all dotplots of a set of sequences - Extract data from PRINTS - Scans proteins using PRINTS - Search and extract from REBASE. Remove restriction sites but maintain the same translation - all-against-all comparison of a set of sequences. Shows info about currently available databases. Shows features of a sequence - Silent mutation restriction enzyme scan - Finds siRNA duplexes in mRNA - Searches a DNA database for matches with a set of STS primers - Finds a match of a large sequence against one or more sequences - Extract data from TRANSFAC database.
Gcghelp shows documentation for a program. Scans DNA sequences for transcription factors - Displays membrane spanning regions - Align nucleic coding regions given the aligned proteins - Trim bits off ends of sequences. Can be done interactively with GCG's seqed. inds neighbouring pairs of features in sequences - Strips out DNA between a pair of vector sequences - Counts words of a specified size in a DNA sequence - Finds all exact matches of a given size between 2 sequences Modified to meet SACS requirements last modified.
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