Right after logging into the cluster, you will find several pre-loaded software. You can find them via module list command. Although you are free to unload them using the module unload command, you should always keep the module cluster/1.0 loaded as it includes essential configurations for running computations in the cluster.
MATLAB Student 7.7.0 was available to download from the developer's website when we last checked. We cannot confirm if there is a free download of this software available. The following versions: 7.7, 7.1 and 7.0 are the most frequently downloaded ones by the program users.
Matlab 7.0.4 Software Free Download
We cannot guarantee that the program is safe to download as it will be downloaded from the developer's website. Before launching the program, check it with any free antivirus software. The program relates to Development Tools. This PC program process the following extensions: ".mat" and ".mdl". Commonly, this program's installer has the following filenames: matlab.exe and meditor.exe etc. The latest version of MATLAB Student is supported on PCs running Windows XP/Vista/7, 32-bit. This tool was originally created by The MathWorks, Inc.
Generating and installing software on the UNIX systems should be done in a similar, consistent fashion. This allows for ease of maintenance and upgrades, broader support between software staff members, and higher levels of security. This document will describe the process of introducing a new software package to the UNIX environment, starting from downloading the source code to the announcement to the mail list.
Phylogenetic Binning tool Phylogenetic binning tool for paper on "Morphology-based phylogenetic binning of the lichen genera Allographa and Graphis via molecular site wieght calibration" by Simon Berger available for download here tech report PDF and paper File Conversion scripts shell script by Andre Aberer for fasta to phylip conversion
matlab programs by Lowie Li for fasta to phylip and phylip to fasta conversion
Wrapper Scripts Apurva Narechania at the American Museum of Natural history has kindly put togetehr a couple of wrapper scripts for RAxML :-) raxml_launch_serially.sh:A simple shell script that launches one job after the other awaitingfor completion of each job.
raxml_nexusPartConvert.pl:A Perl script that parses a partitioned alignment in Nexus formatwith charsets and produces a partition guide file to be fed to RAxMLwith -q. Preliminary - works with DNA or AA, but not the two togetheryet, so not suitable for mixed-molecule data. Unless the output getsredirected to a file with ">", it will appear on screen.
raxml_wrapper.pl:A Perl script that reads a raxml.config file with common runparameters and executes a directory of Phylip alignment files in batch,then outputs the results in another directory. See the documentationwith "perldoc ./raxml_wrapper.pl".
Guy Leonard at Exeter has updated his wrapper environment called easyRax Alexis has developed a couple of perls scripts A perlscript for computing bootstrap branch lengths with RAxML. This script can be used to perform the following task with RAxML: Given abest-known ML tree, generate a number of Bootstrap replicates and justre-estimate the branch lengths for that given fixed tree topology oneach Bootstrap replicate.
To invoke the script call it as follows: "perl bsBranchLengths.pl alignmentFileName treeFileName numberOfReplicates". Thescript assumes that the RAxML executable is located in the directorywhere you execute it. Otherwise, if RAxML is located in your Linux/Unixpath just replace every occurence of "./raxmlHPC"by "raxmlHPC" in thescript. The bootstrapped trees with branch lengths will be written intoa file called "bsTrees".
This script is intended for use with programs that inferdivergencetime estimates.
A perlscript for finding the best protein substitution model Hereis a little perl-script that will automatically determine thebest-scoring AA substitution model on a fixed starting tree. Notethat raxmlHPC must be in your $PATH for this to work.
For unpartitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip > outfile The outfile will then containthe best-scoring AA model to use with RAxML.
For partitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip partitionData.txt > outfile The outfilewill then contain the best-scoring AA model for every partition.
James Munro has written a Guide to install RAxML on MACs Olaf Bininda-Emonds has written batchRAxML.pl. This nice script by my good colleague from Munich times Olaf Bininda-Emonds provides a wrapper around RAxML to easily analyze a set of data files according to a common set of the search criteria. Also organizes the RAxML output into a set of subdirectories. Frank Kauff has written PYRAXML2. Frank Kauff at University of Kaiserslautern (formerly at Duke University) has written this cool script that reads NEXUS-style data files and prepares the necessary input files and command-line options for RAxML-VI-HPC. You can download the BETA-version here: PYRAXML2 It requires PYTHON and BIOPYTHON to be installed on your computer.
RAxML v7.2.8 alpha release source code available here
RAxML v7.2.7 (alpha) available for download here
RAxML v7.2.6 available for download here and here is a windows executable
RAxML v7.2.5 (alpha) available for download here and here is a windows executable
RAxML v7.2.4(alpha) available for download here
RAxML v7.2.3 (alpha) available for download here
RAxML v7.2.2 available for download here and download windows executable
RAxML v7.2.1 (alpha) available for download here windows executable here
RAxML v7.2.0 (alpha) available for download here
RAxML v7.1.0 (alpha) available for download here
RAxML v7.0.4 available for download here
RAxML v7.0.3 available for download here
Windows executable. Graham Jones has provided a nice PDF on How to run RAxML under XP and Vista.
Mac executable (iMAC)
Mac executable (iMAC Pthreads-version)
Mac executable (PowerMac G5)
Mac executable (PowerMac G5 Pthreads-version)
RAxML-VI-HPC (version 2.2.3)and a comprehensive Manual (v2.2.3) RAxML-VI-HPC (version2.0.2) and a comprehensive Manual(v2.0)
RAxML-VI-HPC (version1.0) and a comprehensive Manual(v1.0)
RAxML-VI: Sequential program with significantly accelerated hill-climbing search algorithm for huge alignment data.
RAxML-III: Sequential program, includes more models of nucleotide substitution than RAxML-II.
RAxML-II: Sequential, Parallel, and Distributed implementation of RAxML with less model functionality.
There are also some free third-party software packages you can use to accomplish this. One community-generated solution in the MATLAB File Exchange is Format Tick Labels ( =15986) as an example. It will replace axes tick labels with formatted text objects that can include both Tex and LaTex interpreted strings.
7) Also be aware that the MCR installer may claim that it will install the Microsoft Visual C redistributable. However that never seems to work for me and Dependence Walker will show that it can't find msvcr80.dll and msvcr90.dll. In this case, go to the Microsoft web site and download and install the redistributable yourself. You can also try here: Latest Supported Visual C++ Downloads. After doing that it seems to work most of the time. Sometimes the installer just quits after installing the Visual C++ redistributable and never installs the actual MATLAB run time library software. Some have found that rebooting after that first installation where it quits will allow you to rerun the MCRInstaller.exe and it will then finish. 2ff7e9595c
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