NAME

       phylo_pipeline - Phylo Pipeline of PALEOMIX suite

SYNOPSIS

       paleomix phylo_pipeline <command> [options] [makefiles]

DESCRIPTION

       The  PALEOMIX  pipelines  are  a  set  of  pipelines  and  tools designed to aid the rapid
       processing of High-Throughput Sequencing  (HTS)  data:  The  BAM  pipeline  processes  de-
       multiplexed  reads from one or more samples, through sequence processing and alignment, to
       generate BAM alignment files useful in  downstream  analyses;  the  Phylogenetic  pipeline
       carries  out genotyping and phylogenetic inference on BAM alignment files, either produced
       using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite
       of  analyses  on  low  coverage  equine  alignments,  in  order  to detect the presence of
       F1-hybrids in archaeological  assemblages.  In  addition,  PALEOMIX  aids  in  metagenomic
       analysis of the extracts.

       The  pipelines  have  been  designed with ancient DNA (aDNA) in mind, and includes several
       features especially useful for the analyses of ancient samples, but can  all  be  for  the
       processing of modern samples, in order to ensure consistent data processing.

       phylo_pipeline is the phylo pipeline of paleomix(1).

OPTIONS

   Commands
       phylo_pipeline help
              Display this message.

       phylo_pipeline example [...]
              Copy example project to folder.

       phylo_pipeline makefile
              Print makefile template.

       phylo_pipeline genotype [...]
              Carry out genotyping according to makefile.

       phylo_pipeline msa [...]
              Carry out multiple sequence alignment.

       phylo_pipeline phylogeny
              Carry out phylogenetic inference.

   Optional arguments
       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       --to-dot-file=DOT_FILE
              Write dependency tree to the specified dot-file.

   Progress reporting
       --progress-ui=PROGRESS_UI
              Select method for displaying the progress of the pipeline: 'running' = Display only
              currently running nodes; 'progress' = Display changes in state; 'summary'; one-line
              summary only. [Default is 'running']

       --ui-colors=UI_COLORS
              Enable, disable, or force the use of color codes when printing the command-line UI.
              Unless forced, colors will only be printed if STDOUT is a TTY [Default is 'on']

   Logging
       --log-file=LOG_FILE
              Create the specified log-file and write any messages to this file.  By  default,  a
              log-file will be generated in the folder specified using --temp-root, but only when
              messages are logged

       --log-level=LOG_LEVEL
              Log messages to  log-file  at  and  above  the  specified  level;  one  of  'info',
              'warning', 'error', or 'debug' [warning]

   Scheduling
       --samtools-max-threads=SAMTOOLS_MAX_THREADS
              Maximum number of threads to use when genotyping or building pileups [1]

       --examl-max-threads=EXAML_MAX_THREADS
              Maximum number of threads to use for each instance of ExaML [1]

       --max-threads=MAX_THREADS
              Maximum number of threads to use in total [4]

       --dry-run
              If  passed,  only  a  dry-run  in performed, the dependency tree is printed, and no
              tasks are executed.

   Required paths:
       --temp-root=TEMP_ROOT
              Location for temporary files and folders [/tmp/USERNAME/phylo_pipeline]

       --samples-root=SAMPLES_ROOT
              Location of BAM files for each sample [./data/samples]

       --regions-root=REGIONS_ROOT
              Location of BED files containing regions of interest [./data/regions]

       --prefix-root=PREFIX_ROOT
              Location of prefixes (FASTAs) [./data/prefixes]

       --refseq-root=REFSEQ_ROOT
              Location of reference sequences (FASTAs) [./data/refseqs]

       --destination=DESTINATION
              The destination folder for result files [./results]

   Files and executables:
       --list-input-files
              List all input files used by pipeline for the makefile(s), excluding any  generated
              by the pipeline itself.

       --list-output-files
              List all output files generated by pipeline for the makefile(s).

       --list-executables
              List all executables required by the pipeline, with version requirements (if any).

   Config files:
       --write-config-file
              Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini

SEE ALSO

       paleomix(1)

AUTHOR

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