March 17, 2010

BRAT: bisulfite-treated reads analysis tool

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 1:05 pm
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We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.

Availability: The source code is freely available for download at and is distributed as Open Source software under the GPLv3.0.

March 14, 2010

invertFREGENE: software for simulating inversions in population genetic data

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 1:01 pm
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Inversions are a common form of structural variation, which may have a marked effect on the genome and methods to infer quantities of interest such as those relating to population structure and natural selection. However, due to the challenge in detecting inversions, little is presently known about their impact. Software to simulate inversions could be used to provide a better understanding of how to detect and account for them; but while there are several software packages for simulating population genetic data, none incorporate inversion polymorphisms. Here, we describe a software package, modified from the forward-in-time simulator FREGENE, which simulates the evolution of an inversion polymorphism, of specified length, location, frequency and age, in a population of sequences. We describe previously unreported signatures of inversions in SNP data observed in invertFREGENE results and a known inversion in humans.

March 3, 2010

Phybase: an R package for species tree analysis

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 9:42 am
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Phybase is an R package for phylogenetic analysis using species trees. It provides functions to read, write, manipulate, simulate, estimate, summarize and plot species trees, which contain not only the topology and branch lengths but also population sizes.

Availability: The Phybase package is available at the R repository. The manual and supporting materials including source code, sample R code and sample data files for the species tree analysis are available at

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