LIKEWIND - a maximum likelihood-based method for detecting conflicting phylogenetic signal in nucleotide sequence alignments
covARES - a package of application to map the site rates derived by maximum likelihood into the known structure of models of a homologous protein.
PUZZLEBOOT - allow the analysis of multiple data sets (bootstrapped datasets) with the program TREE-PUZZLE
Expected Likelihoods Weights - implement the method of "expected likelihood weights" devised by Strimmer and Rambaut (2002) to estimate confidence sets of trees.
CONCATERPILLAR - a hierarchical likelihood ratio test for phylogenetic congruence.
BARREL-o-MONKEYS - a series of Python scripts that automate repetitive tasks that are so simple, a monkey could do them.
RAADdet - Rates-across-sites Amino Acid Log-Det
CBOrg - a mitochondrial comparative BLAST for organelles



LIKEWIND

A maximum likelihood-based method for detecting conflicting phylogenetic signal in nucleotide sequence alignments

References:

Archibald, J.M. and A.J. Roger (2002) Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 316:1041-1050.

Archibald, J.M. and A.J. Roger (2002) Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signal. J. Mol. Evol. 55:232-245.

Get the Users Manual here: HTML format or PDF format

To get the latest version of the program you can download the 'tar' file here: Likewind1.0.1.tar .
Once you have down loaded this simply extract the tar file to access the 3 programs:
likewind.pl, getlikes.pl and simblock.pl

Hints on extracting the file in a unix environment. At the prompt type:
$ tar xvomf likewind_1.0.tar
Then the folder should be extracted in the current directory.

If you have any questions, do not hesitate to contact the creators John M. Archibald or
Andrew J. Roger


covARES

covARES is a package of application to map the site rates derived by maximum likelihood into the known structure of models of a homologous protein.

Get more information about covARES here (users manual etc.)

If you have any questions, do not hesitate to contact the creator Christian Blouin

PUZZLEBOOT

Puzzleboot was created by Mike Holder and Andrew Roger to allow the analysis of multiple data sets (bootstrapped datasets) with the program TREE-PUZZLE even though TREE-PUZZLE lacks the "M" option of many PHYLIP programs. It is designed for use with the distance matrix option of TREE-PUZZLE.

The program PUZZLEBOOT version 1.03 is available here as is the README file

Expected Likelihood Weights (elw.pl & calcwts.pl)

The ELW PERL scripts -- elw.pl and calcwts.pl -- were created to implement the method of "expected likelihood weights" devised by Strimmer and Rambaut (2002) to estimate confidence sets of trees.

A tar archive containing these scripts is available here as is the README file

 

 

CONCATERPILLAR

A hierarchical likelihood ratio test for phylogenetic congruence.

The most recent version of Concaterpillar, implementing MPI-based distribution of subprocesses, can be downloaded here.

Get the Users Manual here: TXT format

Features added:

Concaterpillar 1.4:

  • support for nucleotide alignments
  • pre-screening to make sure that all alignment pairs have enough taxa in common
  • added a debug flag (-d, --debug) to print out all output from RAxML in case users are experiencing problems
  • added a cleanup step to remove old RAxML output files that might cause subsequent runs to crash (user will be asked before files are deleted)
  • added an optional flag to allow Concaterpillar to old RAxML output files without asking (-n, --noask)
  • support for "relaxed" Phylip alignment format (not strictly 10 characters per sequence name)

    • Concaterpillar 1.3:

  • fixed some bugs that might be encountered if some of your alignments have extremely different true phylogenies (thanks to Haruo Suzuki for finding this)

    Concaterpillar 1.2:

  • trees are inferred and evaluated using RAxML (faster and more accurate)
  • an improved algorithm for resuming interrupted runs has been implemented
  • an installation script has been added to locate programmes on which Concaterpillar depends
  • support for more substitution models has been added

    • If you use Concaterpillar for a publication, please cite:

    Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008 Feb; 57(1): 104-15.

    The version of Concaterpillar we used for this publication can be downloaded here.

     

    BARREL-o-MONKEYS

    Included in this package are the following applications:

    alvert- alignment format conversion (and related functionality)

    blastmonkey- repetitive online (NCBI) and local BLAST and output parsing

    alignmonkey- automated multiple sequence alignment and cleanup

    QuASAR- recode a sequence alignment with a reduced alphabet

    tresolve- produce a semi-exhaustive list of trees with given constraints

    Download Barrel-o-Monkeys here

     

    RAADdet

    Calculates Log-Det distance between amino acid sequences. It can optionally model variation of rates across sites, and can perform bootstrap replicates prior to calculating distances.

    Download RAADdet here

     

    CBOrg

    A mitochrondrial comparitive BLAST for organelles

    Download CBOrg here