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TCW External References
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External software and databases

The TCW uses the following external software packages, where they are all included with the TCW package except for BLAST and the optional DE methods. Please reference any program in your publications that are used in your analysis.

runSingleTCW

  1. BLAST: is used for assembly and annotation.
    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
  2. Diamond: maybe be used in place of Blast for super-fast annotation.
    Benjamin Buchfink, Chao Xie & Daniel H. Huson, Fast and Sensitive Protein Alignment using DIAMOND, Nature Methods, 12, 59–60 (2015) doi:10.1038/nmeth.3176.
  3. Ublast: maybe used in place of Blast of super-fast annotation.
    Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.
  4. CAP3: is used for assembly.
    Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
  5. UniProt: though other databases can be used for annotation, the TCW has the best support for this database.
    Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, et al. (2012) The UniProt-GO Annotation database in 2011. Nucleic Acids Res 40: D565-570.
  6. Gene Ontology (GO): if UniProt is used, the TCW uses it along with the GO database for GO annotations.
    The GO consortium (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res 40: D559-564.

runDE

The following are all R packages.
  1. edgeR: differential expression (DE) analysis
    Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
  2. DESeq: differential expression (DE) analysis
    Love MI, Huber W and Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550.
  3. GOSeq: GO differential expression
    Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11: R14.

runMultiTCW

  1. ESTscan: to create protein sequences from the nucleotide sequences.
    Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol: 138-148.
  2. orthoMCL: to compute orthologous and paralogous clusters.
    Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
  3. KaKs_calculator: compute Ka/Ks values.
    Zhang Z, Li J, Xiao-Qian Z, Wang J, Wong, G, Yu J (2006) KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Geno. Prot. Bioinfo. Vol 4 No 4. 259-263.

viewMultiTCW

  1. MUSCLE: computes multiple alignment of a cluster (non-applet version only).
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.

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