hrefinder Icon

hrefinder

alpha

Detection of homologous recombination events from SNP data

Add a Review
0 Downloads (This Week)
Last Update:
Download hreFinder.tar.gz
Browse All Files
BSD Linux

Description

This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs differs from the ancestral allele, it may be better explained as a mutation or sequencing error. But if a series of SNP alleles differ from the ancestral pattern, then it may be more likely that an HRE has occurred, particularly if the allele pattern matches that from another part of the tree better than that of the ancestral node.

hrefinder Web Site

Categories

Bio-Informatics

License

BSD License

KEEP ME UPDATED

Other Useful Business Software

The Leading Provider of Business VoIP Phone Systems Icon

Award-Winning Business VoIP Phone System

The Leading Provider of Business VoIP Phone Systems Icon
1 of 5 2 of 5 3 of 5 4 of 5 5 of 5
62 Reviews
  • Unlimited Calling, Faxing, Video Conferencing
  • 24/7 U.S Based Customer Support
  • Super Reliable, Simple to Use
Write a Review

User Reviews

Be the first to post a review of hrefinder!

Additional Project Details

Intended Audience

Science/Research

Programming Language

Python, Perl, C++

Registered

2012-12-03

Thanks for helping keep SourceForge clean.

Screenshot instructions:
Windows
Mac
Red Hat Linux   Ubuntu

Click URL instructions:
Right-click on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)

More information about our ad policies
X

Briefly describe the problem (required):

Upload screenshot of ad (required):
Select a file, or drag & drop file here.

Please provide the ad click URL, if possible:

Get latest updates about Open Source Projects, Conferences and News.

No, thanks