Category: Phylogenetic Analysis

ANGST – ANalyzer of Gene and Species Trees

ANGST

:: DESCRIPTION

AnGST performs a phylogenetic reconciliation between a given species and gene tree, positing the best scoring set of HGT, DUP, and LOS events to explain all topological incongruities between the two trees. In order to protect against phylogenetic noise, we have designed AnGST to be capable of incorporating information from dozens of bootstrap trees simultaneously. In cases of variations among bootstrap subtrees, the subtree that best accords with the reference tree is adopted.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 ANGST

:: MORE INFORMATION

Citation

LA David & EJ Alm.
“Rapid evolutionary innovation during an Archaean Genetic Expansion.”
Nature, 2010. doi:10.1038/nature09649.

AdaptML 1.0 – Partitioning of Gene Sequences according to their Genetic and Ecological Similarity

AdaptML 1.0

:: DESCRIPTION

AdaptML is a software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 AdaptML

:: MORE INFORMATION

Citation

Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.
Resource partitioning and sympatric differentiation among closely related bacterioplankton.
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

phyloMeta 1.3 – Phylogenetic Comparative Analyses with Meta-analysis

phyloMeta 1.3

:: DESCRIPTION

PhyloMeta is a program for integrating a phylogeny (in NEWICK format) into traditional meta-analysis. All the familiar statistics of meta-analysis are calculated (e.g., pooled effect sizes with 95%CI and homogeneity tests) and paired with the phylogenetically-independent equivalents to these statistics.

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 phyloMeta

:: MORE INFORMATION

Citation

phyloMeta: a program for phylogenetic comparative analyses with meta-analysis.
Lajeunesse MJ.
Bioinformatics. 2011 Sep 15;27(18):2603-4. doi: 10.1093/bioinformatics/btr438

PRUNETREE 5.0 – Trimming Taxa Off Phylogenies

PRUNETREE 5.0

:: DESCRIPTION

Prunetree is a program for trimming taxa off phylogenies. You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1).

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

PRUNETREE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PRUNETREE

 :: MORE INFORMATION

Siphy 0.5 – SIte-specific PHYlogenetic analysis

Siphy 0.5

:: DESCRIPTION

Siphy (SIte-specific PHYlogenetic analysis) analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • Java

:: DOWNLOAD

  Siphy

:: MORE INFORMATION

Citation

Manuel Garber et al.
Identifying novel constrained elements by exploiting biased substitution patterns,
Bioinformatics 2009 25(12):i54-i62.

PhyloAcc v1.0 – Bayesian Detection of Changes of Conservation of a Genomic Region

PhyloAcc v1.0

:: DESCRIPTION

PhyloAcc is a software to detect the shift pattern of DNA substitution rate of a genomic region and identify genomic elements accelerated in some specific species from a set of conserved elements.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS
  • R

:: DOWNLOAD

PhyloAcc

:: MORE INFORMATION

Citation

Hu Z, Sackton TB, Edwards SV, Liu JS.
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.
Mol Biol Evol. 2019 May 1;36(5):1086-1100. doi: 10.1093/molbev/msz049. PMID: 30851112; PMCID: PMC6501877.

CLIME v1.1 Beta – Clustering by Inferred Models of Evolution OMIM results

CLIME v1.1 Beta

:: DESCRIPTION

CLIME is an algorithm that partitions an input gene set of interest into distinct, evolutionarily conserved modules (ECMs). It then expands each module with genes sharing an inferred evolutionary history.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS

:: DOWNLOAD

CLIME

:: MORE INFORMATION

Citation

Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK.
Expansion of biological pathways based on evolutionary inference.
Cell. 2014 Jul 3;158(1):213-25. doi: 10.1016/j.cell.2014.05.034. PMID: 24995987; PMCID: PMC4171950.

GFICLEE 1.0 – Gene Function Inferred by Common Loss Evolutionary Events

GFICLEE 1.0

:: DESCRIPTION

GFICLEE is a program for predicting the new members in biological pathway or biological complex. It is based on the common loss events in gene evolution.

::DEVELOPER

Yang Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOS
  • Java

:: DOWNLOAD

GFICLEE

:: MORE INFORMATION

Citation

Fang Y, Li M, Li X, Yang Y.
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.
BMC Genomics. 2021 Oct 29;22(1):774. doi: 10.1186/s12864-021-08070-7. PMID: 34715785; PMCID: PMC8557005.

GGDC 3.0 – Genome-to-Genome Distance Calculator

GGDC 3.0

:: DESCRIPTION

GGDC  is an updated and enhanced version with improved DDH-prediction models and additional features such as confidence-interval estimation. To the best of our knowledge, it is the only digital DDH method that provides this feature. Of all genome-based methods we are aware of, GGDC 2.0 yields the highest correspondence to wet-lab DDH (without sharing DDH’s drawbacks).

::DEVELOPER

Leibniz Institute DSMZ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP1, Auch AF, Klenk HP, Göker M.

RΕQ 2.0 – Assessing branch supports of a Distance-based Phylogenetic Tree with the Rate of Elementary Quartets

RΕQ 2.0

:: DESCRIPTION

REQ is a command line program written in Java that estimates the rate of elementary quartets (REQ) for each internal branch of an unrooted binary phylogenetic tree from a distance matrix.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

RΕQ 

:: MORE INFORMATION