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454tofastq

Converts fasta and qual sequences from 454 to fastq

acc2gb

Shell code to retrieve GenBank records from a list of accession numbers (using gnu-parallel)

codonalign

Generates a codon-based alignment from an amino acid alignment and CDS sequences

competitive_mapping_workflow

Pipeline and workflow for RNA-seq processing, differential expression and allele-specific expression analyses (and more).

compmap

Compares reads mapped to two reference and splits best alignments

concat_fasta

Concatenates multiple FASTA alignments into a single super-matrix

concatfasta

Concatenates FASTA files, imputes dummy sequences, and prints a partition table

distknks

Calculates Kn/Ks distances from two CDS sequences

dna_lstm

LSTM for binary DNA sequence classification

eeb214

Collection of jupyter notebooks for evolutionary biology remote learning

effective_number_of_codons

Calculates de number of effective codons Nc for an unaligned of coding sequences in FASTA format

extractgenbanktoexcel

fasomerecords

Extracts FASTA records from multiFASTA file based on a list of FASTA headers

gb2fasta

Perl script to convert GenBank records to FASTA format

gdrive

Google Drive CLI Client

genetic_drift

Shiny app with a genetic drift simulator

getphased

RANDOMLY sorts out IUPAC ambiguities into different haplotypes

interleave_paired_fastq

Interleaves separated pair-ended FASTQ files

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

jellyfish

A fast multi-threaded k-mer counter

landscape-genetics-r-funtions

A suit of different functions that can be useful for landscape genetics analyses in R

lastz

Mirror of latest lastz from http://www.bx.psu.edu/~rsharris/lastz/ (for automatic cactus installation)

lastz-1

Program for aligning DNA sequences, a pairwise aligner.

lastzwrapper

Bash shell wrapper to build whole-genome alignments with lastz

mask_fastq

Perl/Python scripts that masks bases as "N"s given a PHRED quality score threshold

matepereads

Separates true pairs into 1 and 2 files and saves unpaired reads

microsatellites

R scripts and functions for microsatellite EBSP

myconet

orderfromsamtools

Reorders by-individual consensus FASTQ files into FASTA by-gene alignments

paml_dist