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Sim4
Jul 20, 2023
Algorithm for aligning expressed DNA with genomic sequences
This package implements the Sim4 algorithm for aligning expressed DNA with genomic sequences, described in the paper
L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller 1998 “A computer program for aligning a cDNA sequence with a genomic DNA sequence.” Genome Research 8, 967-974.
Port maintained by the FreeBSD bio-porters mailing list.
Checkout these related ports:
- Wise - Intelligent algorithms for DNA searches
- Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
- Vt - Discovers short variants from Next Generation Sequencing data
- Vsearch - Versatile open-source tool for metagenomics
- Viennarna - Alignment tools for the structural analysis of RNA
- Velvet - Sequence assembler for very short reads
- Vcftools - Tools for working with VCF genomics files
- Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
- Vcf2hap - Generate .hap file from VCF for haplohseq
- Vcf-split - Split a multi-sample VCF into single-sample VCFs
- Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
- Unanimity - Pacific Biosciences consensus library and applications
- Ugene - Integrated bioinformatics toolkit
- Ucsc-userapps - Command line tools from the UCSC Genome Browser project
- Trimmomatic - Flexible read trimming tool for Illumina NGS data