Table 1 List of programs used throughout the paper with a brief description of their function
From: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents
Program | Version | Use | Citation |
|---|---|---|---|
DeconSeq | 0.4.1 | Read filtering and processing | [47] |
Trinity | trinityrnaseq- r2013-02-25 | de novo assembly of Illumina reads | [48] |
gsAssembler | 2.6 | de novo assembly of Illumina and 454 reads | Roche/454 manual |
Bowtie | 1.0.0 | Paired end read mapping implemented in RSEM | [49] |
RSEM | 1.2.0 | Uses bowtie and maximum likelihood approaches to map reads to a scaffold and give the number of reads that map to a sequence | [50] |
DESeq | 1.14 | Uses read counts to test for differential expression | [51] |
MUSCLE | 3.6 | Multiple sequence alignment | [52] |
PAML | 4.7 | Analysis of protein and DNA sequences using maximum likelihood based methods |