PhyDesign – Phylogenetic Informativeness Analysis

PhyDesign

:: DESCRIPTION

PhyDesign is a platform-independent online application that implements the Townsend phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Lopez-Giraldez F., and J.P. Townsend, 2011.
PhyDesign: an online application for profiling phylogenetic informativeness.
BMC Evol. Biol., 11: 152.

chromEvol 2.0 – Analyze Changes in Chromosome-number along a Phylogeny

chromEvol 2.0

:: DESCRIPTION

 chromEvol is a program for analyzing changes in chromosome-number along a phylogeny and for the inference of polyploidy.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

   chromEvol

:: MORE INFORMATION

Citation

Mayrose I, Barker MS, Otto SP. 2010.
Probabilistic models of chromosome number evolution and the inference of polyploidy.
Systematic Biology. 59(2):132-144

phyloExpCM 0.32 – Phylogenetic Analysis with experimentally determined Codon Models

phyloExpCM 0.32

:: DESCRIPTION

phyloExpCM is a Python package to implement experimentally determined codom models of substitution for phylogenetics.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 phyloExpCM

:: MORE INFORMATION

Citation

Bloom JD.
An experimentally determined evolutionary model dramatically improves phylogenetic fit.
Mol Biol Evol. 2014;31:1956-1978.

Pyvolve v1.0.1 – Python Library to Simulate Evolutionary Sequence data

Pyvolve v1.0.1

:: DESCRIPTION

Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pyvolve

:: MORE INFORMATION

Citation

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
Spielman SJ, Wilke CO.
PLoS One. 2015 Sep 23;10(9):e0139047. doi: 10.1371/journal.pone.0139047.

CowPI – A rumen microbiome focussed version of the PICRUSt Functional Inference software

CowPI

:: DESCRIPTION

CowPi consists of a set of pre-calculated files that can be used with an installation of PICRUSt to allow functional predictions to be made from 16S rRNA samples from the rumen microbiome.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A., Siu Ting, K., Hughes, M., Rubino, F., Friedersdorff, M. and Creevey, C., 2018.
CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software.
Frontiers in Microbiology, 9, p.1095.

PICRUSt2 v2.3.0-b -Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

PICRUSt2 v2.3.0-b

:: DESCRIPTION

PICRUSt is a software for predicting functional abundances based only on marker gene sequences.

::DEVELOPER

PICRUSt2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PICRUSt2

:: MORE INFORMATION

Citation

PICRUSt2: An improved and extensible approach for metagenome inference
Gavin M. Douglas, Vincent J. Maffei, Jesse Zaneveld, Svetlana N. Yurgel, James R. Brown, Christopher M. Taylor, Curtis Huttenhower, Morgan G. I. Langille
doi: https://doi.org/10.1101/672295

clan_check v1.3 – Check Trees for compatibility with Defined Clans

clan_check v1.3

:: DESCRIPTION

Clan_Check analyses single-copy phylogenetic trees to assess if they violate clans defined by the user. This is designed for large-scale phylogenomic analyses where the user may have thousands of phylogenetic trees. This tool can help enrich the data for orthologs, by identifying where paralogy has caused violation of “well known” clans in outgroups.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Clan_Check

:: MORE INFORMATION

Citation

Siu-Ting, Karen, et al.
Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.
Molecular biology and evolution (2019).

Clann 4.2.4 – Construct Phylogenetic Supertrees

Clann 4.2.4

:: DESCRIPTION

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.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Clann

:: MORE INFORMATION

Citation:

Creevey C. J. and McInerney, J. O. 2005
Clann: Investigating phylogenetic information through supertree analyses.
Bioinformatics 21 (3): 390-2.

TIGER 1.02 – Identify Rapidly-evolving Characters in Evolutionary Data

TIGER 1.02

:: DESCRIPTION

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.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Python

:: DOWNLOAD

TIGER

:: MORE INFORMATION

Citation:

Cummins, C.A. and McInerney, J.O. (2011)
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.
Systematic Biology 60 (6) 833-844.

ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.851

:: DESCRIPTION

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.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

ModelGenerator

:: MORE INFORMATION

Citation:

Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29