GCUA
General Codon Usage Analysis. The pdf on how to use this program is available
here.
Documentation can be found here.
Download:
Choose your operating system:
Apple (MacOSX)
Apple (not MacOSX)
Digital UNIX
Linux
IBM AIX
Windows
CRANN
Program for detecting adaptive evolutionary events in protein-coding DNA sequences.
Pdf
Manual available here.
Choose your operating system:
Apple (MacOSX)
Apple (not MacOSX)
Linux
Windows
CLANN
Program for constructing phylogenetic supertrees from input trees with overlapping leaf sets.
Pdf
Manual available here.
Download the required version here:
PutGaps
PutGaps is a free software program designed and written by David Fitzpatrick and Melissa Pentony.
The purpose of the program is to add gaps to a DNA alignment file based on its Amino Acid equivalent.
PutGaps has been written in-house using the Java programming language, and will run on MacOS X, Windows and Linux
terminal / MS_DOS windows.
Please note that this is Beta software, there still may be bugs!
PutGaps
Model Generator
ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments.
Download Model Generator.
Startup command:
java -jar modelgenerator.jar alignment_file num_gamma_categories
If you get a java.lang.OutOfMemory error then increase the amount of memory available to java using the -Xmx option (e.g. java -Xmx200m ....)
DPRml
Program for parallelising ML Phylogenetic tree estimation.
pdf
MultiPhyl
MultiPhyl is the first high-throughput implementation of a distributed phylogenetics platform that is capable of using the idle computational resources of many heteogeneous non-dedicated machines to form a phylogenetics supercomputer.
TIGER
TIGER is a new piece of software developed to identify evolutionary rates independantly of a tree. It uses confict or patterns in the data as a proxy for rapid evolution. For more information see the website here.