Software for phylogenetics and mol. evol.

Andrew Rambaut andrew.rambaut at zoology.oxford.ac.uk
Mon Jul 3 08:57:13 EST 2000


Hi, I have just setup a set of ListBot mailing lists for
some of the phylogeny and molecular evolution programs on
our website. These are to advise people who download the
software when new versions are available or about bugs.
You can subscribe to the lists by either emailing the address
below or from the web pages of the respective programs (links
below).

We have had 50-fold more downloads than emails telling us
that a program has been downloaded. Computer programs have
bugs and these may affect your analyses. If we don't know
you have the program, we can't inform you when bugs come to
light. 

You will only get an occasional message (these are not discussion
lists). Subscribe to all the programs you are interested in.
You are free to unsubscribe from the ListBot lists at any time.

Thanks,
Andrew

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Genie - GENIE (Genealogy Interval Explorer) is a program for
the inference of demographic history from reconstructed
phylogenies. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/Genie>

Mailing List:  <mailto://geniesoft-subscribe@listbot.com>

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TreeEdit - TreeEdit is an application for
organising, viewing and manipulating sets of phylogenetic
trees. It is intended as a tool for preparing sets of trees
for use in phylogenetics packages such as PAUP. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/TreeEdit>

Mailing List:  <mailto://treeedit-subscribe@listbot.com>

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TipDate - a program to estimate the rate of molecular evolution and
time-scale of a phylogeny from dated sequences. It includes
the usual range of substitution models. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/TipDate>

Mailing List:  <mailto://tipdate-subscribe@listbot.com>

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LARD - an application for detecting and characterising recombination
between DNA sequences using maximum likelihood. It
accommodates a wide range of substitution models and also
allows for rate heterogeneity between sites. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/Lard>

Mailing List:  <mailto://lardsoft-subscribe@listbot.com>

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QDate - an application for estimating the date of divergence between
two pairs of sequences given that the date of divergence of
the members of each pairs is known. Confidence intervals
about this date can be estimated and the fit of the model
tested. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/QDate>

Mailing List:  <mailto://qdate-subscribe@listbot.com>

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Se-Al - a Macintosh application for creating
multiple sequence alignments from nucleotide and amino acid
sequences. It is intended for the production of hand
alignments and for preparing input for alignment programs
such as CLUSTAL and phylogeny reconstruction programs such
as PAUP. It is particularly useful for manipulating protein
coding DNA/RNA sequences. 

Web page:      <http://evolve.zoo.ox.ac.uk/software/Se-AL>

Mailing List:  <mailto://sealsoft-subscribe@listbot.com>

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Seq-Gen 1.1 - a program that will
simulate the evolution of nucleotide sequences along a
phylogeny. A range of models of molecular evolution are
implemented including the general reversible model (REV).
Site-specific rate heterogeneity may be incorporated in a
number of ways (gamma distributed and codon based).

Web page:      <http://evolve.zoo.ox.ac.uk/software/Seq-Gen>

Mailing List:  <mailto://seqgen-subscribe@listbot.com>


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