bali-phy - Bayesian Inference of Alignment and Phylogeny

       Benjamin Redelings.

                                                    Feb 2018                                         bali-phy(1)

bali-phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon se‐
       quences.  BAli-Phy uses MCMC and Bayesian methods to estimate evolutionary trees, positive selection, and
       branch lengths while averaging over alternative alignments.

       BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using substitution
       models like GTR+gamma.  BAli-Phy automatically estimates relative rates for each gene.

bali-phydna.fasta--smodelgtr
              Analyze sequences in dna.fasta under the GTR model.

       bali-phydna.fasta-Sgtr-Inone
              Perform a traditional fixed-alignment analysis with gaps treated as missing data.

       bali-phydna.fastaamino.fastacodons.fasta-S1:gtr-S2:lg08-S3:gy94
              Perform an analysis of 3 genes where each gene has a different substitution  mode.   The  sequence
              names in all three files must be the same.

       For  each option below, more information is available by specifying the long form of the option as a help
       topic.  For example: bali-phyhelpalphabet-h, –help, –help=topic
              Display a friendly help message.  Specify –help=advanced or –help=expert to display more  advanced
              options.

       -v, –version
              Print version information.

       -t, –test
              Analyze the initial values and exit.

       -V, –verbose, –verboseNUM
              Print  extra output to aid in trouble-shooting.  If NUM is not specified the default is 1.  Values
              from 2 to 4 increase the amount of information displayed.

       -cfilename, –configfilename
              Read commands from filename before command line.

-iNUM, –iterationsNUM
              The number of iterations to run.

       -nSTRING, –nameSTRING
              Name for the output directory to create.

       -xNUM, –subsampleNUM
              Factor by which to subsample.  This option should usually not be used.

       -sNUM, –seedNUM
              Random seed.  Useful for replaying specific runs when trouble-shooting.

-Aalphabet, –alphabetalphabet
              The alphabet.

       -Smodel, –smodelmodel
              The substitution model.

       -Imodel, –imodelmodel
              The insertion-deletion model.

       -Bprior, –branch-lengthsprior
              Prior on branch lengths.

       -Rprior, –scaleprior
              Prior on the scale.

       -LNUMS, –linkNUMS
              Link  partitions.   Takes  a  comma-separated  list of numbers indicating partitions.  For example
              --link1,2,3.

bali-phy - Bayesian Inference of Alignment and Phylogeny

-Tfilename, –treefilename
              File with initial tree in Newick format or NEXUS format.

       -U, –unalign
              Unalign all variable-alignment partitions before starting MCMC instead using the  supplied  align‐
              ment as a starting value.

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

       bp-analyze

bali-physequence-file1 [sequence-file2 ...]  [OPTIONS]

       bali-phy help topic