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Theory of Evolution

Theory of Evolution book

Professor McInerney has contributed a chapter to a newly-published book on “The Theory of Evolution: Principles, Concepts, and Assumptions“.     Details on the book (extracted from the promotional material of the book) Darwin’s nineteenth-century writings laid the foundations for modern studies of evolution, and theoretical developments in the mid-twentieth century fostered the Modern Synthesis. Since […]

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Manchester Evolution Symposium

This is the webpage of the Manchester Evolution Symposium, funded by the Templeton Foundation and the research Domain of Evolution, Systems and Genomics. Organiser: Professor James O. McInerney Key Administrator: Marian Halfpenny Strategic Funding Team Support: Dr. Daniel Jameson Thursday 14th December, Kanaris Theatre 10:30 Arrival, Registration & Coffee 11:00-11:30 Mark Wilkinson ‘Post Phylogenetic Systematics’ […]

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Templeton Foundation Confirms Funding

The John Templeton Foundation have confirmed the award of a two-year research grant to the laboratory of James McInerney at The University of Manchester. The grant will fund two post-doctoral researchers for two years each in order to shed light on the origin of the Eukaryotic cell. This area of research has experienced a huge […]

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Phylogenomics Summer School 2016 (May 29th-June3rd)

UPDATE: THE COURSE FOR 2016 IS NOW OVER [symple_social icon=”twitter” url=”twitter.com/mcinerneylab” title=”Follow Me” target=”blank” rel=””][symple_social icon=”facebook” url=”facebook.com/mcinerneylab” title=”Like or Share” target=”blank” rel=””] Current status of registrations (since April 4th) [wppb progress=100 option=”flat option=”animated-candystripe red” percent=inside fullwidth=true] What?: Week-long, intensive phylogenetics course covering all aspects of bioinformatics and phylogenetics/phylogenomics. Where?: Department of Biology, National University of Ireland […]

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Davide Pisani Seminar on “Evidence that comb jellies are not the sister of all the other animals”

Dr. Davide Pisani from the University of Bristol spoke today about his work using molecular phylogenetics in order to resolve the earliest branches on the Animal tree of life. His talk was based on a recent paper in PNAS from his research group in Bristol and collaborators. http://www.pnas.org/content/112/50/15402.abstract The main thrust of this argument is […]

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Post-doc position available (starting immediately)

There is a post-doc position available in my research group in Ireland. The position is to continue our work on the origins and early evolution of eukaryotes.  In this case, we are going to dig into the metabolism of early eukaryotes.  We will spend time trying to reconstruct ancestral metabolisms, analysing the origins of eukaryote-specific […]

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Bioinformatics and Phylogenetics Summer School 2015

Current State of Registrations: [wppb progress=100 option=”red candystripe” location=inside] We’re full. What?: Week-long, intensive phylogenetics course covering all aspects of bioinformatics and phylogenetics/phylogenomics. Where?: Department of Biology, National University of Ireland Maynooth.  This is approximately 40 minutes from Dublin Airport (Aer Lingus, British Airways, Ryanair, American Airlines, Lufthansa, Air France, etc.) ,  25km from the centre […]

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Phylogenetics Summer Course 2014

Current State of Registrations: What?: Week-long, intensive phylogenetics course covering all aspects of modern molecular phylogenetics and phylogenomics. Where?: Department of Biology, National University of Ireland Maynooth.  This is approximately 40 minutes from Dublin Airport (Aer Lingus, British Airways, Ryanair, American Airlines, Lufthansa, Air France, etc.) ,  25km from the centre of Dublin, Ireland. [symple_googlemap […]

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Among-site rate variation and how to examine it.

Some time ago we published a method for exploring among-site rate variation in evolutionary datasets [1]. This particular problem has been of interest for more than 40 years – some characters in a dataset will evolve at different rates to other characters and this might mislead phylogeny reconstruction. There are a few principal situations where […]

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Eukaryote Origins

In the last five years, there has been tremendous progress made in understanding the origin of the eukaryote cell. This progress has been on a number of fronts – phylogenetic, metabolic and bioenergetic and in terms of other data that relate directly to evolution. Our latest paper in PNAS is, I feel, the latest in […]

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Photographs from Phylogenetics Course in Eirce Sicily, March 2013

From the 10th to the 17th of March, 2013 a course on phylogenetics and phylogenomics was held in the beautiful old village of Erice in Sicily and members of the Bioinformatics and Molecular Evolution Unit participated as lecturers and as practical demonstrators. The course was sponsored by EMBO, the European Molecular Biology Organisation.   [ready_google_map […]

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Mechanisms of Protein Evolution SMBE Satellite Meeting, Denver February 2013

Several members of the Bioinformatics and Molecular Evolution Unit attended the second “Mechanisms of Protein Evolution” meeting in Denver Colorado in February 2013. The agenda for the meeting is here:   http://www.proteinevolution.org/wp-content/uploads/2012/09/Agenda_MPEII_5Feb13.pdf   During the meeting a video was made where a number of the speakers gave a brief overview of what they were speaking […]

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Pervasive horizontal gene transfer in Chlamydia

The genome era has really taught us something impressive about the plasticity of bacterial genomes. Gene exchange between strains of the same species and gene exchange between different species is not limited to special categories of genes and is not limited to ‘oddball’ species.  It is pervasive, frequent and it is also a public health […]

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Clans, clades and unrooted trees

A few years back, Mark Wilkinson at The Natural History Museum, London came up with the idea that we should really have a more precise language for groups that we can see on unrooted trees. The problem stemmed from the fact that on an unrooted tree a clade is not defined. A clade is a […]

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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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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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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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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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