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AliStat version 1.3
AliStat has been written to allow users to evaluate how complete their multiple sequence alignments (MSA) of nucleotides or amino acids are.
In particular, AliStat allows a user to generate four useful metrics (i.e. the completeness of an MSA (Ca), of a row in an MSA (Cr), of a column in an MSA (Cc), and of homologous sites in a sub-alignment of s... moreequences i and j (Cij)), each of which will tell the user something useful about the distribution of missing data in an MSA.
The information thus obtained can be used to make educated decisions about how the data in the MSA should be analysed phylogenetically.
The output is a set of informative figures, tables, and sub-alignments.
In addition, AliStat produces information that meets the Minimum Reporting Standard (MRS) for MSAs, a concept that we introduce in Wong TFK, Kalyaanamoorthy S, Meusemann K, Yeates DK, Misof B, Jermiin LS. 2017. AliStat: Quality-control metrics for multiple sequence alignments. Nature Methods (in prep). less
multi sequence alignments (MSA)
This software was developed by the bioinformatics and phylogenomics team in Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia.
This project is a collaboration between the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia, and ZFMK, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany.
CSIRO Open Source Software Licence (Based on MIT/BSD Open Source Licence)
Wong, Thomas KF; Kalyaanamoorthy, Subha; Meusemann, Karen; Yeates, David; Misof, Bernhard; Jermiin, Lars (2014): AliStat version 1.3. v1. CSIRO. Software Collection.
All Rights (including copyright) CSIRO 2014.
The metadata and files (if any) are available to the public.
Tested on Linux and MacOS
CLSD Strategic: Solving Biodiversity Cha
We generate knowledge on the mechanistic links and synergistic interactions between landscape change, species invasions and native species resilience in terrestrial ecosystems. Working on both natural and agricultural systems, we undertake research and develop theory to underpin more effective policy and management actions for conservation, invasio... moren and production challenges in the face of rapid global change. less
Bioinformatics software previously made available from the CSIRO ICT and Services website.
Thomas KF Wong
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