GIPhy

Inferring alien oligonucleotides (adapters, primers, ...) from FASTQ file

Fast removal of contaminating reads from FASTQ file(s)

Fast trimming of sequencing reads

Assembling SSU

Block Mapping and Gathering with Entropy

Translating and back-translating codon and amino-acid sequence files

COG annotation of CDS

Building a supermatrix of characters from a set of multiple sequence alignments

Estimating standard descriptive statistics from contig sequences

delineation cutoff estimates

Translating the maximum number of codons using the minimum number of ORFs

Extracting CDS from contig sequences

Extracting a nucleotide segment from a FASTA-formatted file

Creating an AGP file from a FASTA-formatted scaffold sequence file

Estimating standard descriptive statistics from FASTQ files

Find characters shared by a group of aligned sequences

building forests of near-ML trees

Genome de novo assembly from raw paired-end FASTQ files

Preprocessing FASTQ files

Finding Repeats Using BLAST