List of the software
version 2.2.31+
Basic Local Alignment Search Tool (BLAST) is probably the most popular similarity search tool. Sequence similarity searching is one of the more important bioinformatics activities and often provides the first evidence for the function of a newly sequenced gene or piece of sequence.
blastn blastp blastx tblastn
makeblastdb blastdbcmd
DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.
diamond makedb --in nr.faa -d nr diamond blastp -d nr -q proteins.fna -o output
version 2.8.2
The SRA Toolkit will allow you to programmatically access data housed within SRA and convert it from the SRA format to the other formats.
use the version installed in the opt
/opt/sratoolkit.2.8.2-1-ubuntu64/bin/
version 4.6
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cdhit cdhit-2d cdhit-454 cdhit-est cdhit-est-2d cd-hit-2d-para cd-hit-div cd-hit-para
version 6.6.0.0
EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
version 2.3.2 (hmm2)
version 3.1b2 (hmm)
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
hmmalign ` hmmbuild ` hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch
version 2.0.0
Accurate inference of orthologous gene groups made easy. “OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy”
orthofinder
tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.
Biopython is a set of freely available tools for biological computation written in Python.
version 3.9.6
CMake is an extensible, open-source system that manages the build process in an operating system and in a compiler-independent manner.