Comments for Bioinformatics and Molecular Evolution Unit

Comment on TIGER by TIGER 1.02 - Identify Rapidly-evolving Characters in Evolutionary Data

TIGER 1.02 - Identify Rapidly-evolving Characters in Evolutionary Data — Fri, 20 Jan 2012 03:49:18 +0000

[...] TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted in order to improve phylogenetic reconstruction. When a site is changing very quickly between taxa it might not hold much phylogenetic information and therefore might simply be a source of noise. Use of TIGER can (a) allow you to see the amount of rapid evolution and noise in your alignment and (b) provide a quick and easy way to remove as many of the “noisy” sites as possible. [...]

Comment on putgaps by PutGaps Beta - DNA Gapped File from Amino Acid Alignment

PutGaps Beta - DNA Gapped File from Amino Acid Alignment — Fri, 20 Jan 2012 03:41:12 +0000

[...] PutGaps is a software to add gaps to a DNA alignment file based on its Amino Acid equivalent. [...]

Comment on GCUA: General Codon Usage Analysis by GCUA 1.2 - Evaluate Codon Usage in a set of Genes

GCUA 1.2 - Evaluate Codon Usage in a set of Genes — Fri, 20 Jan 2012 03:39:09 +0000

[...] GCUA （General Codon Usage Analysis） is designed to perform various tasks that are of use for evaluating codon usage in a set of genes. You can get it to do some simple things like calculate the number of observations of a particular codon in a gene. Or you can do the same thing for the combined dataset. You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole). The program also produces a distance matrix based on the similarity of codon usage in genes. [...]

Comment on Crann: A program for detecting adaptive evolution in protein-coding DNA sequences by Crann 1.04 - Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04 - Detect Adaptive Evolution in Protein-coding DNA Sequences — Fri, 20 Jan 2012 03:34:16 +0000

[...] Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user. [...]

Comment on clann by Clann 3.2.2 - Construct Phylogenetic Supertrees

Clann 3.2.2 - Construct Phylogenetic Supertrees — Fri, 20 Jan 2012 03:29:38 +0000

[...] Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees. [...]

Comment on ModelGenerator by ModelGenerator 0.85 - Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.85 - Amino Acid & Nucleotide Substitution Model Selection — Fri, 20 Jan 2012 03:27:07 +0000

[...] ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models. [...]

Comment on Dr. David Fitzpatrick by Post-doctoral applicants sought for IRCSET grants. | Bioinformatics and Molecular Evolution Unit

Sat, 19 Nov 2011 15:55:30 +0000

[...] Fitzpatrick Lab [...]

Comment on Dr. Davide Pisani by Post-doctoral applicants sought for IRCSET grants. | Bioinformatics and Molecular Evolution Unit

Sat, 19 Nov 2011 14:45:45 +0000

[...] Pisani Lab [...]

Comment on James McInerney by Survival of the sexiest | Bioinformatics and Molecular Evolution Unit

Survival of the sexiest | Bioinformatics and Molecular Evolution Unit — Wed, 09 Nov 2011 11:43:24 +0000

[...] is to announce that on Tuesday next (the 15th of November), there will be a talk given by Dr. James McInerney in JH2 in the John Hume Building at NUI Maynooth at 7:30, [...]

Comment on Tardigrades in light of new evidence by Karen

Karen — Sat, 24 Sep 2011 19:31:59 +0000

excellent work! well done guys!!