DendroPy: a Python library for phylogenetic computing
...s, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful ph...2202 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...llop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improv...rom reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviat...2187 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative info...2160 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likel...2179 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...nd flanking base pairs of each such structural feature. The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. Th...2172 days ago
2095 days ago
NanoPack: visualizing and processing long-read sequencing data
...GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Ma...2092 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity...1997 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1967 days ago
NanoPack: visualizing and processing long-read sequencing data
...the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Ma...1955 days ago