Category: Phylogenetic Analysis

OrthoSelect – Selection of Orthologs in Phylogenomics

OrthoSelect

:: DESCRIPTION

OrthoSelect is a easy-to-install and easy-to-use tool for finding ortholog groups in EST databases. It automatically searches assembled EST sequences against databases of ortholog groups (OG), assigns ESTs to these pre-defined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified ortholog sequences and others the possibility to further process this alignment in a last step. OrthoSelect performes better than the best-hit selection strategy and shows reliable results re-annotating database member sequences of OrthoMCL-DB and KOG. Since a correct orthology assignment is a important prerequisite for the construction of reliable data sets, OrthoSelect is capable of producing such data sets. This makes a OrthoSelect a valuable tool for researcher dealing with large EST libraries focussing on constructing data sets for phylogenetic reconstructions.

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OS X
  • Perl

:: DOWNLOAD

OrthoSelect

:: MORE INFORMATION

Citation

F. Schreiber, K. Pick, D. Erpenbeck, G. W?rheide, B. Morgenstern (2009)
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
BMC Bioinformatics 10, 219

Treephyler 1.1 – Fast Taxonomic Profiling of Metagenomes.

Treephyler 1.1

:: DESCRIPTION

Treephyler is a tool for fast taxonomic profiling of metagenomes. It combines the predictive power of tree-based and speed of signature-based approaches. Treephyler was evaluated on a real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Treephyler

:: MORE INFORMATION

Citation

F. Schreiber, P. Gumrich , R. Daniel and P. Meinicke (2010)
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics 26, 960-961

Phylodendron 0.8d – Phylogenetic Tree Drawing

Phylodendron 0.8d

:: DESCRIPTION

Phylodendron is a java software for drawing phylogenetic trees. Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology. It will read tree data in New Hampshire (Newick) format, then display graphical views of the phylogenetic tree. Various options allow you to modify, adorn and edit the tree. Standard application functions to save, print, edit and manage preferences are included. This program will not estimate nor produce the tree data. For that, software such as Phylip, Clustal W, and others may be used.

Phylodendron Online Version

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Phylodendron

:: MORE INFORMATION

N/A

GRate 1.0 – Relative Rate Test for Groups of Taxa Using General DNA Substitution Models in PAUP*

GRate 1.0

:: DESCRIPTION

GRate is a software for relative rate tests with groups supporting all models of nucleotide substitution known by PAUP*.

::DEVELOPER

Kai Müller

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

GRate

:: MORE INFORMATION

Citation

Müller K, Borsch T, Legendre L, Porembski S, Theisen I, Barthlott W
Evolution of carnivory in Lentibulariaceae and the Lamiales
Plant Biology 2004, 6:477-490

BootFam – Define Gene/Protein Families

BootFam

:: DESCRIPTION

BootFam takes as input a set of homologous protein sequences, a species tree, and a sequence-to-species mapping. The output is a set of gene families relative to the species tree.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

BootFam Source Code

:: MORE INFORMATION

BootFam is distributed under the GNU General Public License.

 

LAPD – Estimate Protein Distances

LAPD

:: DESCRIPTION

LAPD estimates pairwise distances for a set of protein sequences. The output can be used in conjunction with other phylogeny programs.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

LAPD Source Code

:: MORE INFORMATION

lapd is distributed under the GNU General Public License.

PrIME-GSR 1.0 – Bayesian Integrated Model

PrIME-GSR 1.0

:: DESCRIPTION

primeGSR is a program for gene tree inference that takes a known species tree into account. It is based on GSR, a probabilistic model integrating gene duplication, sequence evolution and a relaxed molecular clock for substitution rates, and efficient algorithms that enables genome-wide analysis of gene families.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrIME-GSR

:: MORE INFORMATION

Citation:

Åkerborg, Sennblad, Arvestad, Lagergren, Gene tree analysis using a Bayesian integrated model for genes, sequences, and rates, submitted.

map_dp – Factorize Branchlengts

map_dp

:: DESCRIPTION

map_dp is a software to factorize branchlengths into time and rates.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

map_dp

:: MORE INFORMATION

Citation:

Åkerborg O, Sennblad B, Lagergren J (2008) Birth-death prior on phylogeny and speed dating. BMC Evol Biol 8, 77

primeGEM 0.2 – Probabilistic Orthology Analysis

primeGEM 0.2

:: DESCRIPTION

primeGEM is a program that performs probabilistic orthology analysis (Arvestad et al. 2003, 2004, submitted, Sennblad and Lagergren, 2009). It computes for a pair of genes the probability that they are orthologous (note that this correpsponds to the probability that their least common ancestor is a speciation). It is based on the gene evolution model which models gene duplication and loss using a generalized birth-death model with threee parameters. The parameters can be integrated over using MCMC or (soon) maximized over using ML.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

primeGEM

:: MORE INFORMATION

Citation:

Sennblad, Lagergren, 2009, Probabilistic orthology analysis, Systematic Biology (2009) 58 (4): 411-424.

PrIMETV 1.5.6 – PrIME Tree Viewer

PrIMETV 1.5.6

:: DESCRIPTION

PrIMETV is a program that can visualize tree-within-tree phenomena such as gene/species tree reconciliations. Output can be given in a range of formats.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows with cygwin

:: DOWNLOAD

PrIMETV

:: MORE INFORMATION

Citation:

Sennblad B et al (2007) primetv: a viewer for reconciled trees. BMC Bioinformatics 8, 148