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Software

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Contents

Aliscore

Quality check for alignments.

COGNATE

COGNATE: Comparative Gene Annotation characterizatorCOGNATE is a tool to simultaneously analyze a given protein-coding gene annotation and the corresponding assembled sequences of a genome. It allows a quick and easy extraction of basic genome feature and gene repertoire data.

DiStats

The Perl script DiStats simplifies the task of preparing DNA barcode data releases.

AMARE

Tool to assess the reliability of AFLP markers and for optimization of the signal-to-error ratio of the AFLP binary character matrices: (Kück et al. 2012).

MARE

Tool to assess potential information content of your data set and select an optimal data subset by new reduction heuristics.

FASconCAT

Concatenation of sequence files: (Kück & Meusemann 2010).

FASconCAT-G

Offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes.

MultimoSeqSim

Simulation of sequence evolution allowing different evolutionary models on different branches of the tree.

SAMS

Splits Analysis MethodS.

AliGROOVE

AliGROOVE determines and visualizes the content of potentially randomized sequence similarities and alignment ambiguities in multiple sequence alignments. In addition, AliGROOVE can tag potentially unreliable branches of given topologies (Kück et al. submitted).

Utilities

A few useful tools for alignment and tree reconstruction.

Links

Secondary Structure Analyses