REFGEN and TREENAMER: Automated sequence data handling for phylogenetic analysis in the genomic era

Evolutionary Bioinformatics

Volumn 2009, Issue 1, 2009, Pages 1-4

  Leonard, Guy ^a   Stevens, Jamie R ^a   Richards, Thomas A ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Branch labels; Phylogeny; Sequence alignment; Text management

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PROGRAM; GENBANK; GENE SEQUENCE; GENOMICS; HUMAN; HUMAN GENOME PROJECT; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE DATABASE;

EID: 70349103849     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article

References (11)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-410.
2. Gribaldo S, Philippe H. Ancient phylogenetic relationships. Theoretical Population Biology. 2002;61:391-408.
3. Cusimano N, Zhang LB, Renner SS. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Mol Biol Evol. 2008;25:265-276.
4. Horner DS, Embley TM. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol Biol Evol. 2001;18:1970-1975.
5. Dacks JB, Marinets A, Doolittle WF, Cavalier-Smith T, Logsdon JM Jr. Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang. Mol Biol Evol. 2002;19:830-840.
6. Keane TM, Creevey CJ, Naughton TJ, Pentony MM, Naughton TJ, Mcinerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2004;6:29.
7. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics. 1989;5:164-166
8. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003; 52:696-704.
9. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572-1574.
10. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-2690.
11. Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), Version 4, Sunderland, Massachusetts, Sinauer Associates. 2002.