| Name | Description | Origin | Version | References |
|---|---|---|---|---|
| BLAST | BLAST (basic local alignment search tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. | https://blast.ncbi.nlm.nih.gov/Blast.cgi | 2.6.0 | Camacho, C., Boratyn, G. M., Joukov, V., Vera Alvarez, R., & Madden, T. L. (2023). ElasticBLAST: accelerating sequence search via cloud computing. BMC bioinformatics, 24(1), 1-16. |
| Phylogenetic tree | MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. | http://www.drive5.com/muscle/ | 3.8.31 | Edgar, R. C. (2021). MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping. BioRxiv 2021.06.20.449169. |
| Genewise | GeneWise compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. | https://www.ebi.ac.uk/Tools/psa/genewise/ | wise2-4-1 | Birney, E., & Durbin, R. (2000). Using GeneWise in the Drosophila annotation experiment. Genome Research, 10(4), 547-548. |
| Colinearity | This document describes installation and usage of the LASTZ sequence alignment program. LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ's command-line syntax. That is, it supports all of BLASTZ's options but also has additional ones, and may produce slightly different alignment results. | http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/_README.lastz-1.02.00.html | 1.02.00 | Harris, R. S. (2007) Improved Pairwise Alignment of Genomic DNA. Pennsylvania State University, University Park, PA. |
| Primer Design | Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. | https://primer3.ut.ee/ | 4.1.0 | Kõressaar, T., Lepamets, M., Kaplinski, L., Raime, K., Andreson, R., & Remm, M. (2018). Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics, 34(11), 1937-1938. |
| CIPRES | CIPRES (Cyberinfrastructure for Phylogenetic Research) is the premiere online resource for Phylogenetics, Systematics, and Evolutionary Biology. It offers a user-friendly platform designed to facilitate phylogenetic research, providing researchers with access to high-performance computing resources for phylogenetic analysis. | https://www.phylo.org/ | / | Miller, M. A., Pfeiffer, W., & Schwartz, T. (2011, July). The CIPRES science gateway: a community resource for phylogenetic analyses. In Proceedings of the 2011 TeraGrid Conference: extreme digital discovery (pp. 1-8). |
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