PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifyin...1412 days ago
1412 days ago
1402 days ago
G-NEST: The Gene NEighborhood Scoring Tool
The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.1369 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polym...several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-se...as well as linkage disequilibrium, recombination, gene flow a...1308 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), use...richment of TFs and cofactors in gene bodies and flanking regions i...ri binary classification of genes as targets or non-targets. W...urons divided by Immediate Early Gene expres...1307 days ago
1259 days ago
1250 days ago
gggenomes: A grammar of graphics for comparative genomics
gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.1240 days ago
1214 days ago