Provided by: hyphy-pt_2.5.52+dfsg-1_amd64 bug

NAME

       hyphy - Hypothesis testing using Phylogenies (pthreads version)

DESCRIPTION

       usage:  hyphy  or  HYPHYMPI  [-h]  [--help][-c]  [-d]  [-i] [-p] [BASEPATH=directory path]
       [CPU=integer] [LIBPATH=library path] [USEPATH=library path] [<standard analysis  name>  or
       <path to hyphy batch file>] [--keyword value ...] [positional arguments ...]

       Execute a HyPhy analysis, either interactively, or in batch mode optional flags:

       -h --help
              show this help message and exit

       -c     calculator mode; causes HyPhy to drop into an expression evaluation until 'exit' is
              typed

       -d     debug mode; causes HyPhy to drop into an expression  evaluation  mode  upon  script
              error

       -i     interactive mode; causes HyPhy to always prompt the user for analysis options, even
              when defaults are available

       -p     postprocessor  mode;  drops  HyPhy  into  an   interactive   mode   where   general
              post-processing scripts can be selected upon analysis completion

       -m     write diagnostic messages to messages.log

   optional global arguments:
       BASEPATH=directory path
              defines the base directory for all path operations (default is pwd)

       CPU=integer
              if  compiled  with OpenMP multithreading support, requests this many threads; HyPhy
              could use fewer than this but never more; default is the number of  CPU  cores  (as
              computed by OpenMP) on the system

       LIBPATH=directory path
              defines  the  directory  where  HyPhy  library files are located (default installed
              location is /usr/local/lib/hyphy or as configured during CMake installation

       USEPATH=directory path
              specifies the optional working and relative path directory (default is BASEPATH)

       ENV=expression
              set   HBL   environment   variables   via   explicit   statements    for    example
              ENV='DEBUG_MESSAGES=1;WRITE_LOGS=1'

       batch file to run
              if specified, execute this file, otherwise drop into an interactive mode

       analysis arguments
              if  batch  file  is  present, all remaining positional arguments are interpreted as
              inputs to analysis prompts

       optional keyword arguments (can appear  anywhere);  will  be  consumed  by  the  requested
       analysis

       --keyword value
              will  be  passed  to  the analysis (which uses KeywordArgument directives) multiple
              values for the same keywords are  treated  as  an  array  of  values  for  multiple
              selectors

       usage examples:

   Select a standard analysis from the list :
              hyphy -i

       Run a standard analysis with default options and one required user argument;

              hyphy busted --alignment path/to/file

       Run a standard analysis with additional keyword arguments

              hyphy busted --alignment path/to/file --srv No

       See which arguments are understood by a standard analysis

              hyphy busted --help

       Run a custom analysis and pass it some arguments

              hyphy path/to/hyphy.script argument1 'argument 2'

       Available standard keyword analyses (located in /home/nilesh/packages/hyphy/hyphy/res/)

       meme   [MEME]  Test  for  episodic site-level selection using MEME (Mixed Effects Model of
              Evolution).

       mh     Merge two datafiles by combining sites (horizontal merge).

       mv     Merge two datafiles by combining sequences (vertical merge).

       mcc    Compare mean within-clade branch length or pairwise divergence between two or  more
              non-nested cladesd in a tree

       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).

       mgvsgy Compare  the  fits  of  MG94  and GY94 models (crossed with an arbitrary nucleotide
              bias) on codon data.

       mt     Select an evolutionary model for nucleotide data, using the methods of  'ModelTest'
              - a program by David Posada and Keith Crandall.

       fel    [FEL] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood).

       fubar  [FUBAR]  Test  for  pervasive  site-level selection using FUBAR (Fast Unconstrained
              Bayesian AppRoximation for inferring selection).

       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).

       faa    Fit a multiple fitness class model to amino acid data.

       fmm    "Fit  a  model  that  permits  double   (and   triple)   instantaneous   nucleotide
              substitutions"

       fst    Compute various measures of F_ST and (optionally) perform permutation tests.

       slac   [SLAC]  Test  for  pervasive  site-level  selection  using  SLAC (Single Likelihood
              Ancestor Counting).

       sm     Peform a classic and structured Slatkin-Maddison test for the number migrations.

       sns    Parse  a  codon  alignment   for   ambiguous   codons   and   output   a   complete
              list/resolutions/syn and ns counts by sequence/position

       sw     Perform a sliding window analysis of sequence data.

       sa     Perform  a  phylogeny  reconstuction  for  nucleotide,  protein  or codon data with
              user-selectable models using the method of sequential addition.

       sbl    Search an alignment for a single breakpoint.

       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/)

       busted [BUSTED]  Test  for  episodic  gene-wide  selection   using   BUSTED   (Branch-site
              Unrestricted Statistical Test of Episodic Diversification).

       bgm    [BGM]  Apply  Bayesian  Graphical  Model  inference  to  substitution  histories at
              individual sites.

       bva    Run  a  selection  analysis  using  a  general  discrete  bivariate  (dN  AND   dS)
              distribution; the appropriate number of rate classes is determined automatically.

       brp    Interpret bivariate codon rate analysis results.

       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.

       bst    Use  the  improved  branch-site  REL  method of Yang and Nielsen (2005) to look for
              episodic selection in sequences.

       bt     Test whether a branch (or branches) in the tree evolves under different dN  and  dS
              than the rest of the tree.

       absrel [aBSREL]  Test  for lineage-specific evolution using the branch-site method aBS-REL
              (Adaptive Branch-Site Random Effects Likelihood).

       acd    Analyse codon data with a variery of standard models using given tree.

       ad     Analyse nucleotide or aminoacid data with a variery of standard models using  given
              tree.

       adn    Analyse di-nucleotide data with a variery of standard models using given tree.

       afd    Analyse  nucleotide  data  with  a  variery  of  standard  models using given tree,
              estimating equilibrium frequencies as parameters

       ana    Run a selection analysis.

       ai     Peter Simmonds' Association Index (AI).

       relax  [RELAX] Test for relaxation of selection pressure along a  specified  set  of  test
              branches using RELAX (a random effects test of selection relaxation).

       red    Replace sufficiently close sequence with their MRCA

       rpc    Interpret analysis results.

       rmv    Remove sequences with stop codons from the data.

       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.

       rclk   Test for the presence of a global molecular clock on the tree. The tree  is  rooted
              at every possible branch.

       rr     Use relative rate test on three species and a variety of standard models

       rrt    Use relative ratio test on 2 datasets and a variety of standard models

       prime  [PRIME]

       protein
              Compare the fit of several amino-acid substitution models to an alignment using AIC
              and c-AIC.

       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.

       prrti  Given  a list of files (and optionally genetic code tables), perform relative ratio
              tests on all possible pair of the data files.

       pdf    Read sequence data, select a contiguous subset of sites  and  save  it  to  another
              datafile.

       phb    Run  an  example  file  from  our  book  chapter in 'The Phylogentic Handbook' (2nd
              edition).

       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.

       parris A PARtitioning approach for Robust Inference of Selection (written by K. Scheffler)

       contrast-fel
              [Contrast-FEL]  "Perform  a  site-level test for differences in selective pressures
              between predetermined sets of branches."

       conv   Translate an in-frame codon alignment to proteins.

       corr   Assess the correlation  between  phylogenetic  and  compartment  segregation  using
              generalized correlation coefficients and permutation tests.

       cod    Compare  all  203 reversible nucleotide models composed with MG94 to extend them to
              codon data, and perform LRT and AIC model selection.

       cmp    Use a series of LR tests to decide if dN and dS rate distributions are the same  or
              different between two codon alignments.

       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.

       clg    Remove 'gappy' sites from alignments based on a user-specified gap threshold.

       cln    Convert sequence names to HyPhy valid identifiers if needed and replace stop codons
              with gaps in codon data if any are present.

       clsr   Partition sequences into clusters based on a distance matrix.

       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.

       leisr  Infer relative evolutionary rates on a nucleotide or protein alignment, in a spirit
              similar to Rate4Site (PMID: 12169533).

       lz     Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences

       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.

       lht    A Likelihood Ratio Test to detect conflicting phylogenetic signal  Huelsenbeck  and
              Bull, 1996. [Contributed by Olivier Fedrigo].

       tc     Test whether a group of sequences in a sample cluster together

       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!

       dtr    Read sequence data (#,PHYLIP,NEXUS) and convert to a different format

       dist   Generate a pairwise sequence distance matrix in PHYLIP format.

       kh     Perform a Kishino-Hasegawa test on two competing phylogenies

       ub     Obtain an upper bound on the likelihood score of a dataset.

       nuc    Compare all 203  reversible  nucleotide  models  and  perform  LRT  and  AIC  model
              selection.

       nj     Perform  a  phylogeny  reconstuction  for  nucleotide,  protein  or codon data with
              user-selectable models using the method of neighbor joining.

       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.

       gard   [GARD] Screen an alignment using GARD (requires an MPI environment).

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.