University of South Carolina
Biological Sciences Home Page


Hughes Lab Bioinformatics Resource

SNPGenie
A program to estimate evolutionary parameters from pooled next-generation sequencing (NGS) data.


Polyana
A program to detect natural selection in protein-coding sequences by estimating gene diversity at individual nucleotide sites.


Chaos Game
A program based on chaos game representation for analyzing phylogeny of viral sequences.


Supplementary Material for article in Emerging Infectious Diseases (2010) : Reassortment of Ancient Neuraminidase and Recent Hemagglutinin in Pandemic (H1N1) 2009 Virus

Supplementary Table 1

Supplementary Table 2

Supplementary Table 3

Supplementary Table 4

 

SCR3
A program to estimate the synonymous and nonsynonymous differences by the Nei and Gojobori method (1986) and conservative and radical amino acids differences by Hughes et al. (1990) method.

Dblox
Dblox performs a non-overlapping window analysis in a genome to identify the numbers of gene families shared between windows.

Paralogs_data.xls
Microsoft Excel table of recently diverged paralogous genes in human and mouse. This is supplementary information for "Recent Mammalian Gene Duplications: Robust Search for Functionally Divergent Gene Pairs", by Hughes and Friedman.

Supplementary Material for article in Applied Bioinformatics (2006):
Supplementary Table S1.zip
Supplementary Table S2.zip
Supplementary Table S3.zip
Supplementary Table S4.zip

Any suggestions or questions, contact Austin Hughes, at austin@biol.sc.edu