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Showing content from http://www.exelixis-lab.org/web/software/raxml/ below:

The Exelixis Lab

When using RAxML please cite the following paper: A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014, open access.

Get the most up-to-date RAxML version from github.

Please send all your questions and feature request to the RAxML google group. Before posting, keep in mind that a google group actually has a search function! Emails to Exelixis lab members regarding RAxML will not be answered. Messages posted via github will also not be answered.

Since datasets are getting larger here is a formula to estimate RAxML memory requirements: Given an alignment of n taxa and m distinct patterns the memory consumption is approximately:

• MEM(AA+GAMMA) = (n-2) * m * (80 * 8) bytes
• MEM(AA+CAT) = (n-2) * m * (20 * 8) bytes
• MEM(DNA+GAMMA) = (n-2) * m * (16 * 8) bytes
• MEM(DNA+CAT) = (n-2) * m * (4 * 8) bytes

To convert bytes to MB or GB you can use this

You may also use th on-line calculator below:

Required size:

(n-2) * m * (x * 8) bytes = MEM

Web-Servers for phylogenetic placement of short sequence reads (including alignment and visualization tools):

• advanced Swiss Server with pre-computed trees, please cite this paper when using it
• basic German Server without pre-computed trees, please cite this paper when using it

• Daniele Silvestro and Ingo Michalak at the Senckenberg Museum and Research Center have started developing a GUI for RAxML that runs under MACs, Windows, and Linux. The code for the GUI is available here. Please send suggestions and comments to Daniele Silvestro at senckenberg de
• Jacek Kominek from the University of Gdansk in Poland has developed this nice GUI here

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

tech report

and

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 awaiting for completion of each job.
• raxml_nexusPartConvert.pl: A Perl script that parses a partitioned alignment in Nexus format with charsets and produces a partition guide file to be fed to RAxML with -q. Preliminary - works with DNA or AA, but not the two together yet, so not suitable for mixed-molecule data. Unless the output gets redirected to a file with ">", it will appear on screen.
• raxml_wrapper.pl: A Perl script that reads a raxml.config file with common run parameters and executes a directory of Phylip alignment files in batch, then outputs the results in another directory. See the documentation with "perldoc ./raxml_wrapper.pl".

at Exeter has updated his wrapper environment called

has developed a couple of perls scripts

A

for computing bootstrap branch lengths with RAxML. This script can be used to perform the following task with RAxML:

• Given a best-known ML tree, generate a number of Bootstrap replicates and just re-estimate the branch lengths for that given fixed tree topology on each Bootstrap replicate.
• To invoke the script call it as follows: "perl bsBranchLengths.pl alignmentFileName treeFileName numberOfReplicates".  The script assumes that the RAxML executable is located in the directory where you execute it. Otherwise, if RAxML is located in your Linux/Unix path just replace every occurence of "./raxmlHPC" by "raxmlHPC" in the script. The bootstrapped trees with branch lengths will be written into a file called "bsTrees". 
• This script is intended for use with programs that infer divergence time estimates.

A

for finding the best protein substitution model

• Here is a little perl-script that will automatically determine the best-scoring AA substitution model on a fixed starting tree.  Note that 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 contain the best-scoring AA model to use with RAxML.
• For partitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip partitionData.txt > outfile The outfile will then contain the best-scoring AA model for every partition.

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

• test datasets available here

• test datasets available here

• Click here for a table with the experimental raw data

• Initial and final optimization phase of RAxML for an alignment with 150 sequences
• Program Flow of P-Rec-I-DCM-3(RAxML)
• Speedup value: Time to complete one iteration of P-Rec-I-DCM3 for datasets 1-5 and 1 up to 16 processors

• 1,000 taxa plot alignment Alignment of 1,000 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München
• 1,497 taxa plot Alignment of 1,497 Bacteria by Josh Wilcox, Pace Lab, University of Colorado at Boulder, for more information on this alignment please contact the Pace Lab
• 1,663 taxa plot alignment Alignment of 1,663 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München
• 1,728 taxa plot alignment Alignment of 1,728 Archaea by Chuck Robertson, Pace Lab, University of Colorado at Boulder
• 2,000 taxa plot alignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell
• 2,560 taxa plot alignment upon request via email Kallersjo, M., et al., Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl. Syst. Evol., 1998. 213: p. 259-287.
• 4,114 taxa plot alignment 16S ribosomal Actinobacteria RNA sequences, by Usman Roshan, New Jersey Institute of Technology
• 6,722 taxa plot alignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell
• 7,769 taxa plot alignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell
• 8,780 taxa plot alignment Alignment of 8,780 sequences from the ARB database containing Eucarya, Bacteria, Archaea. Original alignment by Harald Meier, TU München, modified by Usman Roshan, New Jersey Institute of Technology
• 25,057 taxa plot alignment Alignment of 25,057 Protobacteria, by Usman Roshan, New Jersey Institute of Technology

The old Alignment Benchmark set: includes some large real-world alignments and best-known trees for those alignments

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