Survival of the sexiest

This 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 7:30pm, entitled:   Survival of the sexiest: Why females want a mate with a good sense of humour, a brightly coloured tail […]

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SMBE2012 in Dublin

The annual meeting of the Society for Molecular Biology and Evolution will be held in Dublin next June from the 23rd to the 26th. In the coming week we will make the decisions on which symposia will be included in the final programme. This will be a great thing on one hand, because we get […]

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Research returns to Ireland far exceed investment

by Dick Ahlstrom, Irish Times Financial returns from Ireland’s expenditure in research have easily outstripped the original investment, according to a study released on 19 September. It claims that while the Exchequer put in almost €1.2 billion over the period 2000-2006 the returns amounted to about €1.8bn. The study by PA Consulting said that the […]

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PVC bacteria are not half-way to being eukaryotes

Over the past few years, manuscripts have been appearing in the literature that have been suggesting that PVC (Planctomycetes, Verrucomicrobia, Chlamydia) bacteria are in many ways like Eukaryotes and consequently, they are an excellent system for understanding eukaryote biology and indeed this group of bugs actually gave rise to modern eukaryotes. This is complete nonsense. […]

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TIGER: Identifying rapidly-evolving characters in evolutionary data.

TIGER: Identifying rapidly-evolving characters in evolutionary data. About TIGER 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 […]

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Pisani lab work on Tardigrades.

Today the Irish Independent ran a nice report on Davide Pisani’s recent publication on the phylogenetic position of Tardigrades.  The work is reported in Proceedings of the National Academy of Sciences, USA.  Here’s the link.

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Goods thinking versus tree-thinking

Goods-thinking versus Tree-thinking In the famous Monty Python “Dead Parrot” sketch, John Cleese returns to a pet shop where he has just bought a parrot and asks for his money back.  The reason being that the parrot is in fact dead. This seems to be a not unreasonable request on the part of the purchaser […]

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CLANN: Software for inferring phylogenetic supertrees.

CLANN: Software for inferring phylogenetic supertrees. What is clann? Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Molecular Evolution Unit at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of […]

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Scientific American Article features Our Cancer Evolution Work

Carl Zimmer has written a very nice article for Scientific American where he discusses the influence of evolution on cancer.  He interviewed Dr. McInerney about his work with Dr. Mary O’Connell of DCU on how natural selection influences genes that are known to be involved in cancer.  The article can be read by clicking on […]

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ModelGenerator: amino acid and nucleotide substitution model selection

ModelGenerator is a a free, easy-to-use model selection program, designed and written by Thomas Keane, that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models. Modelgenerator uses the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC) and hierarchical Likelihood-ratio tests […]

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CRANN: Software for inferring selection

CRANN Crann (pronounced ‘crown’) is the Irish word for ‘tree’. The program 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 […]

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PutGaps : DNA gapped file from Amino Acid alignment

PutGaps : DNA gapped file from Amino Acid alignment Copyright © David Fitzpatrick, Melissa Pentony 2004 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 […]

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GCUA: General Codon Usage Analysis

GCUA: General Codon Usage Analysis GCUA was initially written while working at the Natural History Museum, London. The pdf describing the program can be downloaded here. You can find the project on GitHub here: https://github.com/mcinerneylab/GCUA Purpose: This program is designed to perform various tasks that are of use for evaluating codon usage in a set of genes.  You […]

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