Phylogenetic Tree Inference (Topo) Analysis of Evolutionary Rates (BL) Concordance factor of genes (gCFs) Concordance factor of sites (sCFs) Phylogenetic signal (PS) |
Topo and BL |
RaxML |
Stamatakis, 2006Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
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IQTree |
Nguyen et al., 2015Nguyen LT, Schmidt HA, Von Haeseler A and Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268-274.; Minh et al., 2020bMinh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A and Lanfear R (2020b) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530-1534.
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MrBayes |
Ronquist & Huelsenbeck, 2003Ronquist F and Huelsenbeck JP (2003) Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
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BEAST |
Drummond & Rambaut, 2007Drummond AJ and Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.; Bouckaert et al., 2014Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C H, Xie D, Suchard MA, Rambaut A and Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537.
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BL |
aaML |
PAML |
Yang, 2007Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
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gCFs |
IQTree |
Minh et al., 2020aMinh BQ, Hahn MW and Lanfear R (2020a) New methods to calculate concordance factors for phylogenomic datasets. Mol Biol Evol 37(9):2727-2733.
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sCFs |
IQTree |
Mo et al., 2023Mo YK, Lanfear R, Hahn MW and Minh BQ (2023) Updated site concordance factors minimize effects of homoplasy and taxon sampling. Bioinformatics 39:btac741.
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PS |
SH-test |
CONSEL |
Shimodaira and Hasegawa, 2001Shimodaira H and Hasegawa M (2001) CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
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Correlations between morphotypes and sequence rates |
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Forward Genomics |
Hiller et al., 2012Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR and Bejerano G (2012) A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep 2:817-823.; Prudent et al., 2016Prudent X, Parra G, Schwede P, Roscito JG and Hiller M (2016) Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences. Mol Biol Evol 33:2135-2150.
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TraitRateProp |
Levy et al., 2017Levy KE, Wicke S, Pupko T and Mayrose I (2017) An integrated model of phenotypic trait changes and site-specific sequence evolution. Syst Biol 66:917-933.
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TraitRELAX |
Halabi et al., 2020Halabi K, Levy Karin E, Guéguen L and Mayrose I (2020) TraitRELAX - A codon model for associating phenotypic traits with altered selective patterns of sequence evolution. Syst Biol 70:608-622.
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RERconverge |
Kowalczyk et al., 2019Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL and Chikina M (2019) RERconverge: An R package for associating evolutionary rates with convergent traits. Bioinformatics 35:4815-4817.
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Coevol |
Lartillot & Poujol, 2011Lartillot N and Poujol R (2011) A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol Biol Evol 28:729-744.
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PhyloAcc |
Hu et al., 2019Hu Z, Sackton TB, Edwards SV and Liu JS (2019) Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Mol Biol Evol 36:1086-1100.
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PhyloAcc-GT |
Yan et al., 2022Yan H, Hu Z, Thomas G, Edwards SV, Sackton TB and Liu JS (2022) PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance. bioRxiv. DOI: 10.1101/2022.12.23.521765. https://doi.org/10.1101/2022.12.23.52176...
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Ancestral state reconstruction |
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make.simmap/phytools |
R |
Revell, 2012Revell LJ (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217-223.
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baseML or codeML |
PAML |
Yang, 2007Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
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Selection tests (Branch/Clade Model) |
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codeML |
PAML |
Yang, 2007Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
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aBSREL |
HyPhy |
Smith et al., 2015Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K and Pond SLK (2015) Less is more: An adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 32:1342-1353.
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BUSTED |
Murrell et al., 2015Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM et al. (2015) Gene-wide identification of episodic selection. Mol Biol Evol 32:1365-1371.
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RELAX |
Wertheim et al., 2015Wertheim JO, Murrell B, Smith MD, Pond SLK and Scheffler K (2015) RELAX: Detecting relaxed selection in a phylogenetic framework. Mol Biol Evol 32:820-832.
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Selection Tests (Branch-site Model) |
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codeML |
PAML |
Yang, 2007Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
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FEL |
HyPhy |
Pond et al., 2005Pond SLK and Frost SDW (2005) Not so different after all: A comparison of methods detecting amino acid sites under selection. Mol Biol Evol 22:1208-1222.
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FUBAR |
Murrell et al., 2013Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Pond SLK and Scheffler K (2013) FUBAR: A fast, unconstrained Bayesian approximation for inferring selection. Mol Biol Evol 30:1196-1205.
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MEME |
Murrell et al., 2012Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K and Pond SLK (2012) Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8:e1002764.
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SLAC |
Pond et al., 2005Pond SLK and Frost SDW (2005) Not so different after all: A comparison of methods detecting amino acid sites under selection. Mol Biol Evol 22:1208-1222.
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