BaCoCa 1.1 – Heuristic software tool for Parallel Assessment of Sequence Biases in hundreds of Gene and Taxon Partitions

BaCoCa 1.1

:: DESCRIPTION

BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions.

::DEVELOPER

Centre for Molecular Biodiversity Research (ZMB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Perl
  • R

:: DOWNLOAD

 BaCoCa

:: MORE INFORMATION

Citation

Mol Phylogenet Evol. 2014 Jan;70:94-8. doi: 10.1016/j.ympev.2013.09.011. Epub 2013 Sep 25.
BaCoCa–a heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions.
Kück P1, Struck TH.

TIPP – Taxon Identification and Phylogenetic Profiling

TIPP

:: DESCRIPTION

TIPP is a new marker-based method developed for abundance profiling of metagenomic data.  TIPP uses a collection of 30 universal marker genes and bins the fragments to the marker genes.  For each set of fragments binned to a marker gene, TIPP classifies the fragments by inserting the fragments into the taxonomic tree estimated on the marker gene.  TIPP performs classification in a phylogenetic framework, and thus relies on a reference alignment and tree on full length sequences of known organisms belonging to the same gene, from which fragments are being classified.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TIPP

:: MORE INFORMATION

Citation

TIPP:Taxonomic Identification and Phylogenetic Profiling.
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T.
Bioinformatics. 2014 Oct 29. pii: btu721.

EBD 1.0.8 – Taxon- and Phylogenetic-based Beta Diversity Measures

EBD 1.0.8

:: DESCRIPTION

EBD (Express Beta Diversity) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

  EBD

:: MORE INFORMATION

Citation

Parks, D.H. and Beiko, R.G.
Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.
ISME J. 2013 Jan;7(1):173-83

TAXNAMECONVERT 2.4 – Rename Sequence and Taxon names in Tree and Sequence files

TAXNAMECONVERT 2.4

:: DESCRIPTION

Taxnameconvert is a commandline software that takes as input a file with a name table and usually a Newick formatted tree file or fasta sequence/alignment file, but can also be used to exchange names in many other text file formats.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • Perl

:: DOWNLOAD

 Taxnameconvert

:: MORE INFORMATION