"","Run a standard selection inference method on coding-sequence data.","!Selection Analyses";
"MEME","[MEME] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution).","SelectionAnalyses/MEME.bf";
"FEL","[FEL] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood).","SelectionAnalyses/FEL.bf";
"SLAC","[SLAC] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting).","SelectionAnalyses/SLAC.bf";
"FUBAR","[FUBAR] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection).","SelectionAnalyses/FUBAR.bf";
"BUSTED","[BUSTED] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification).","SelectionAnalyses/BUSTED.bf";
"aBSREL","[aBSREL] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood).","SelectionAnalyses/aBSREL.bf";
"RELAX","[RELAX] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation).","SelectionAnalyses/RELAX.bf";
"FADE","[FADE] Test a protein alignment for directional selection towards specific amino acids along a specified set of test branches using FADE (a FUBAR Approach to Directional Evolution).","SelectionAnalyses/FADE.bf";

"","A collection of tools for evolutionary hypothesis testing coding-sequence data.","!Evolutionary Hypothesis Testing";
"Contrast-FEL","Use a FEL method to test which sites in a gene may be associated with adaptation to a different environment.","SelectionAnalyses/FEL-contrast.bf";

"","Evolutionary rates on non-coding data.","!Relative evolutionary rate inference";
"LEISR","Infer relative evolutionary rates on a nucleotide or protein alignment, in a spirit similar to Rate4Site (PMID: 12169533).","LEISR.bf";

"","Identify pairs or networks of sites that co-evolve.","!Coevolutionary analysis";
"BGM","[BGM] Apply Bayesian Graphical Model inference to substitution histories at individual sites.","BGM.bf";


"","Perform a maximum likelihood analysis on a single file given a single tree.","!Basic Analyses";
"ACD","Analyse codon data with a variery of standard models using given tree.","AnalyzeCodonData.bf";
"AD","Analyse nucleotide or aminoacid data with a variery of standard models using given tree.","AnalyzeNucProtData.bf";
"ADN","Analyse di-nucleotide data with a variery of standard models using given tree.","AnalyzeDiNucData.bf";
"AFD","Analyse nucleotide data with a variery of standard models using given tree, estimating equilibrium frequencies as parameters","AnalyzeNucDataFreq.bf";

"","Perform codon-based positive selection tests using the models of Kosakovsky Pond and Muse (2005).","!Codon Selection Analyses";
"ANA","Run a selection analysis.","dNdSRateAnalysis.bf";
"BVA","Run a selection analysis using a general discrete bivariate (dN AND dS) distribution; the appropriate number of rate classes is determined automatically.","BivariateCodonRateAnalysis.bf";
"CMP","Use a series of LR tests to decide if dN and dS rate distributions are the same or different between two codon alignments.","dNdSDistributionComparison.bf";
"BRP","Interpret bivariate codon rate analysis results.","CodonBivariateRateProcessor.bf";
"RPC","Interpret analysis results.","dNdSResultProcessor.bf";

"","Various tools for checking subdivision of sequences into sub-populations (e.g. HIV-1 compartmentalization), selection operating along the segregating branch etc.","!Compartmentalization";
"AI","Peter Simmonds' Association Index (AI).","SimmondsAI.bf";
"BSEL","Split a tree into two clades (compartments) and a separating branch and test for equality of dN/dS between compartments and for selection along the separating branch using a series of Likelihood Ratio Tests.","SelectionLRT.bf";
"CORR","Assess the correlation between phylogenetic and compartment segregation using generalized correlation coefficients and permutation tests.","TreeCorrelationCoefficients.bf";
"FST","Compute various measures of F_ST and (optionally) perform permutation tests.","F_ST.bf";
"SM","Peform a classic and structured Slatkin-Maddison test for the number migrations.","SM-2019.bf";
"TC","Test whether a group of sequences in a sample cluster together","TestClade.bf";

"","Tools for manipulating sequence files.","!Data File Tools";
"CALN","Align coding sequences to reference (assuming star topology) using a codon-based dynamic programming algorithm (good for fixing multiple frameshifts). Designed with within-patient HIV sequences in mind.","SeqAlignmentCodon.bf";
"CLG","Remove 'gappy' sites from alignments based on a user-specified gap threshold.","CleanGaps.bf";
"CLN","Convert sequence names to HyPhy valid identifiers if needed and replace stop codons with gaps in codon data if any are present.","CleanStopCodons.bf";
"CLSR","Partition sequences into clusters based on a distance matrix.","ClusterByDistanceRange.bf";
"CONV","Translate an in-frame codon alignment to proteins.","CodonToProtein.bf";
"DTR","Read sequence data (#,PHYLIP,NEXUS) and convert to a different format","ConvertDataFile.bf";
"MH","Merge two datafiles by combining sites (horizontal merge).","MergeSites.bf";
"MV","Merge two datafiles by combining sequences (vertical merge).","MergeSequences.bf";
"PDF","Read sequence data, select a contiguous subset of sites and save it to another datafile.","PartitionDataFile.bf";
"RMV","Remove sequences with stop codons from the data.","CleanStopCodons.bf";

"","Miscellaneous items.","!Miscellaneous";
"FAA","Fit a multiple fitness class model to amino acid data.","FitnessAAModels.bf";
"KH","Perform a Kishino-Hasegawa test on two competing phylogenies","KHTest.bf";
"LZ","Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences","LZ_Complexity.bf";
"MCC","Compare mean within-clade branch length or pairwise divergence between two or more non-nested cladesd in a tree","TestCladeMeans.bf";
"PHB","Run an example file from our book chapter in 'The Phylogentic Handbook' (2nd edition).","Miscellaneous/phylohandbook/Phylohandbook.bf";
"RBLE","Use a series of random effects branch-site models to perform robust model-averaged branch length estimation under a codon model with episodic selection.","BranchSiteRELMultiModel.bf";
"RED","Replace sufficiently close sequence with their MRCA","ReduceDataSetMatrix.bf";
"SNS","Parse a codon alignment for ambiguous codons and output a complete list/resolutions/syn and ns counts by sequence/position","SandNSAmbigs.bf";
"SW","Perform a sliding window analysis of sequence data.","SlidingWindowAnalysis.bf";
"UB","Obtain an upper bound on the likelihood score of a dataset.","UpperBound.bf";

"","Compare various models applied to a dataset/tree combination.","!Model Comparison";
"COD","Compare all 203 reversible nucleotide models composed with MG94 to extend them to codon data, and perform LRT and AIC model selection.","CodonModelCompare.bf";
"MGvsGY","Compare the fits of MG94 and GY94 models (crossed with an arbitrary nucleotide bias) on codon data.","MGvsGY.bf";
"MT","Select an evolutionary model for nucleotide data, using the methods of 'ModelTest' - a program by David Posada and Keith Crandall.","ModelTest.bf";
"NUC","Compare all 203 reversible nucleotide models and perform LRT and AIC model selection.","NucModelCompare.bf";
"Protein","Compare the fit of several amino-acid substitution models to an alignment using AIC and c-AIC.","AAModelComparison.bf";


"","Molecular Clock Tests.","!Molecular Clock";
"MCLK","Test for the presence of a global molecular clock on the tree using its root (the resulting clock tree is unrooted, but one of the root branches can be divided in such a way as to enforce the clock).","MolecularClock.bf";
"LCLK","Test for the presence of a local molecular clock. Every subtree of the given tree is subjected to the clock constraint, while the remainder of the tree is free of the clock constraint.","LocalMolClock.bf";
"RCLK","Test for the presence of a global molecular clock on the tree. The tree is rooted at every possible branch.","MolClockAllRoots.bf";


"","Reconstruct a phylogenetic tree using either distance or ML based heuristic methods.","!Phylogeny Reconstruction";
"CLST","Apply clustering methods for phylogeny reconstruction (UPGMA,WPGMA,complete or minimal linkage) to nucleotide, protein and codon data, using MLE of pairwise distances with user-selectable models. These methods produce trees with global molecular clock.","ClusterAnalysis.bf";
"DIST","Generate a pairwise sequence distance matrix in PHYLIP format.","DistanceMatrix.bf";
"NJ","Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of neighbor joining.","NeighborJoining.bf";
"SA","Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of sequential addition.","SequentialAddition.bf";
"TS","Perform an exhaustive tree space search for nucleotide or protein data with user-selectable models. Should only be used for data sets with less than 10 taxa!","TopologySearch.bf";

"","Perform codon-based positive selection tests.","!Positive Selection";

"BST","Use the improved branch-site REL method of Yang and Nielsen (2005) to look for episodic selection in sequences.","YangNielsenBranchSite2005.bf";
"BT","Test whether a branch (or branches) in the tree evolves under different dN and dS than the rest of the tree.","TestBranchDNDS.bf";
"NY","Test for positive selection using the approach of Nielsen and Yabg, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1.","NielsenYang.bf";
"PSM","Test for positive selection using the approach of Nielsen and Yang, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1. Multiple subsets of one data set with shared dN/dS.","MFPositiveSelection.bf";

"","Test for recombination.","!Recombination";
"GARD","[GARD] Screen an alignment using GARD (requires an MPI environment).","GARD.bf";
"GRDR","Process GARD results.","GARDProcessor.bf";
"LHT","A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo].","LHT.bf";
"SBL","Search an alignment for a single breakpoint.","SingleBreakpointRecomb.bf";
"SPL","Plot genetic distances (similarity) of one sequence against all others in an alignment, using a sliding window. Optionally, determine NJ-based clustering and bootstrap support in every window. This is a HyPhy adaptation of the excellent (but Windows only tool) SimPlot (and/or VarPlot) written by Stuart Ray (http://sray.med.som.jhmi.edu/SCRoftware/simplot/)","SimilarityPlot.bf";

"","Test for selection in presence of recombination.","!Selection/Recombination";
"PARRIS","A PARtitioning approach for Robust Inference of Selection (written by K. Scheffler)","PARRIS.bf";

"","Perform relative rate tests.","!Relative Rate";
"RR","Use relative rate test on three species and a variety of standard models","RelativeRate.bf";
"PRR","Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file. ","PairwiseRelativeRate.bf";

"","Perform relative ratio tests.","!Relative Ratio";
"RRT","Use relative ratio test on 2 datasets and a variety of standard models","RelativeRatio.bf";
"PRRTI","Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";
