NAME

       bali-phy - Bayesian Inference of Alignment and Phylogeny

SYNOPSIS

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

       bali-phy help topic

DESCRIPTION

       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.

GENERAL OPTIONS

       For  each option below, more information is available by specifying the long form of the option as a help
       topic.  For example: bali-phy help alphabet

       -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, –verbose NUM
              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.

       -c filename, –config filename
              Read commands from filename before command line.

MCMC OPTIONS

       -i NUM, –iterations NUM
              The number of iterations to run.

       -n STRING, –name STRING
              Name for the output directory to create.

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

       -s NUM, –seed NUM
              Random seed.  Useful for replaying specific runs when trouble-shooting.

PARAMETER OPTIONS

       -T filename, –tree filename
              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.

MODEL OPTIONS

       -A alphabet, –alphabet alphabet
              The alphabet.

       -S model, –smodel model
              The substitution model.

       -I model, –imodel model
              The insertion-deletion model.

       -B prior, –branch-lengths prior
              Prior on branch lengths.

       -R prior, –scale prior
              Prior on the scale.

       -L NUMS, –link NUMS
              Link  partitions.   Takes  a  comma-separated  list of numbers indicating partitions.  For example
              --link 1,2,3.

EXAMPLES

       bali-phy dna.fasta --smodel gtr
              Analyze sequences in dna.fasta under the GTR model.

       bali-phy dna.fasta -S gtr -I none
              Perform a traditional fixed-alignment analysis with gaps treated as missing data.

       bali-phy dna.fasta amino.fasta codons.fasta -S 1:gtr -S 2:lg08 -S 3: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.

REPORTING BUGS

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

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

SEE ALSO

       bp-analyze

AUTHORS

       Benjamin Redelings.

                                                    Feb 2018                                         bali-phy(1)