PerM 0.4.0 – Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data

PerM 0.4.0

:: DESCRIPTION

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PerM

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.

PERM 1.0 – Detect Structuring Factors in meaningful Social Units

PERM 1.0

:: DESCRIPTION

PERM is a permutation program designed to detect statistical connections between grouping structures and grouping factors or correlates. PERM offers four procedures: i) Detecting a statistical link between a collection of groups and some pairwise relationship statistic such as Rxy, Mxy, half or fullsibship; ii) Comparing average values among groups for some measure or statistic; iii) Searching for connections between group structure and category e.g. population membership; iv) Detecting a statistical connection between mating couple formation and some pairwise relationship between partners such as allelic distance on an MHC locus.

:: DEVELOPER

Dr Louis Bernatchez

:: SCREENSHOTS

perm

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

 PERM

:: MORE INFORMATION

Citation

DUCHESNE, P., C. éTIENNE, L. BERNATCHEZ. 2006.
PERM: A computer program to detect structuring factors in meaningful social units.
Molecular Ecology Notes. 6: 965-976.