Aliscore

Description

It has been demonstrated, that random similarity of sequences or sequence sections can impede phylogenetic ananlyses or the identification of gene homology. Additionally, randomly similar sequences or ambiguously aligned sequence sections can negatively interfere with the estimation of substitution model parameters. Phylogenetic studies have shown, that bisases in model estimation and tree reconstructions do not disappear even with large data, but in fact can become pronounced. It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions.

Different approaches have been already suggested to identify and treat problematic alignment sections. We propose an alternative method, which can identify random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. In consequence, consensus profiles identify dominating patterns of non-random similarity or randomness within sections of multiple sequence alignments.

License

GNU GPL v2 or later.

Usage

Aliscore 2.0 is available as part of Bioperl module: Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of bioperl and load default version of bioperl as

module avail bioperl/ # list available modules
module load bioperl   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail bioperl

and choose explicit version you want to use.

perl /software/bioperl/1.6.9/gcc/bin/Aliscore.02.2.pl -h

Documentation

https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf

Homepage

https://www.zfmk.de/en/research/research-centres-and-groups/aliscore