References
- SaitouNNeiMThe neighbor-joining method: A new method for reconstructing phylogenetic treesMol Biol Evol1987444064253447015
- YangKZhangLPerformance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstructionNucleic Acids Res2008365e3318296485
- WhelanSInferring treesKeithJMBioinformatics, Volume 1: Data, Sequence Analysis and EvolutionTotowa, NJHumana Press2008
- EdgarRCMUSCLE: Multiple sequence alignment with high accuracy and high throughputNucleic Acids Res20043251792179715034147
- MorgensternBDIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignmentBioinformatics199915321121810222408
- NotredameCHigginsDGHeringaJT-Coffee: A novel method for fast and accurate multiple sequence alignmentJ Mol Biol2000302120521710964570
- ThompsonJDHigginsDGGibsonTJCLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Res19942222467346807984417
- LassmannTSonnhammerELKalign – an accurate and fast multiple sequence alignment algorithmBMC Bioinformatics2005629816343337
- SnelBBorkPHuynenMGenome evolution. Gene fusion versus gene fissionTrends Genet200016191110637623
- HerniouEALuqueTChenXUse of whole genome sequence data to infer baculovirus phylogenyJ Virol200175178117812611483757
- HouseCHFitz-GibbonSTUsing homolog groups to create a whole-genomic tree of free-living organisms: An updateJ Mol Evol200254453954711956692
- DutilhBESnelBEttemaTJHuynenMASignature genes as a phylogenomic toolMol Biol Evol20082581659166718492663
- MilosavljevićADiscovering sequence similarity by the algorithmic significance methodProc Int Conf Intell Syst Mol Biol199312842917584347
- ChenXKwongSLiMA compression algorithm for DNA sequences and its applications in genome comparisonGenome Inform Ser Workshop Genome Inform1999105161
- ChenXLiMMaBTrompJDNA Compress: Fast and effective DNA sequence compressionBioinformatics200218121696169812490460
- WuXCaiZWanXFHoangTGoebelRLinGNucleotide composition string selection in HIV-1 subtyping using whole genomesBioinformatics200723141744175217495995
- LuGZhangSFangXAn improved string composition method for sequence comparisonBMC Bioinformatics20089Suppl 6S1518541050
- GaoLQiJWhole genome molecular phylogeny of large dsDNA viruses using composition vector methodBMC Evol Biol200774117359548
- KarlinSBurgeCDinucleotide relative abundance extremes: A genomic signatureTrends Genet19951172832907482779
- StuartGWMoffettKBakerSIntegrated gene and species phylogenies from unaligned whole genome protein sequencesBioinformatics200218110010811836217
- QiJWangBHaoBIWhole proteome prokaryote phylogeny without sequence alignment: A K-string composition approachJ Mol Evol200458111114743310
- FelsensteinJPHYLIP – Phylogeny Inference Package (Version 3.2)Cladistics19895164166
- SwoffordDLPAUP*.Phylogenetic Analysis Using Parsimony (*and Other Methods).Version 4Sunderland, MASinauer Associates2003
- The Universal Fingerprinting Chip Applications Server Available at: http://biomedbiotec.encb.ipn.mx/UFCVH/Accessed Dec 22, 2010
- RicePLongdenIBleasbyAEMBOSS: The European Molecular Biology Open Software SuiteTrends Genet200016627627710827456
- TamuraKDudleyJNeiMKumarSMEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0Mol Biol Evol20072481596159917488738
- Reyes-LopezMAMéndez-TenorioAMaldonado-RodríguezRDoktyczMJFlemingJTBeattieKLFingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridizationNucleic Acids Res200331277978912527788
- NeiMKumarSMolecular Evolution and PhylogeneticsNew York, NYOxford University Press2000
- FelsensteinJInferring PhylogeniesSunderland, MASinauer Associates2003
- NyeTMLiòPGilksWRA novel algorithm and web-based tool for comparing two alternative phylogenetic treesBioinformatics200622111711916234319
- FloresRRandlesJWOwensRABar-JosephMDienerTOSubviral agents: ViroidsFauquetCMMayoMAManiloffJDesselbergerUBallLAVirus Taxonomy. VIIIth Report of the International Committee on Taxonomy of VirusesNew York, NYElsevierAcademic Press2005