has developed a couple of perls scripts
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
for finding the best protein substitution model
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.
to install RAxML on MACs
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.
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
PYTHON and BIOPYTHON to be installed on your computer.