Phylosift website – update info about output files

Went through the updated list of output files with Guillaume. Here are the deets for all the files now being created in the PS_temp directory for each run:


protein coding markers

  • *1.unmasked – aligned protein with no masking – not used in downstream analyses
  • *codon.updated.1.fasta – nucleotide, aligned and masked
  • *.newCandidate.aa.1 – same file (unaligned version of hits)
  • *.updated.1.fasta – protein, aligned and masked

.1 refers to chunk number – so if you have duplicate files with .2, etc


  • .1.unmasked – aligned nucleotide ith no masking
  • .short.1.fasta – alignment using cmalign, with masking
  • .long.1.fasta – will we have this too? and sep file for unmasked long sees?

Do we get two .unmasked files if we have a mix of short and long sequences?

no unaligned file in alignDir for 16S/18S data


  • marker_summary.txt – how many hits per marker for each gene

Search mode –keep_search – flag that retains all the search info in the BLAST directory; automatically retains the temp blast files

–keep_search – just undocumented, need to document this under output for all mode


  • enolase.codon.updated.sub1.1.jplace — nucleotide jplace
  • enolase.updated.1.jplace — aa jplace

How is the information from codon and aa trees used in phylosift summaries?

Main output directory – Krona reports

  • filename_allmarkers.html – all markers in treeDir with jplaces
  • filename.html – core markers DNGNGWU only
  • filename.jnlp – javascript of FAT tree visualization
  • filename.xml – fat tree viz itself?

Main output directory – summary files

  • marker_summary.txt – based off of the taxon summary files
  • run_info.txt – going to be updated in the next few days; lists commands and md5 sums and step completion status (start/end time and duration for each chunk at each step – search, align, place, summarize)
  • sequence_taxa_summary.1.txt – summary of chunk
  • sequnce_taxa_summary.txt – combined info from all chunks
  • sequence_taxa.1.txt – summary of chunk
  • sequence_taxa.txt – combined information from all the chunks
  • taxa_90pct_HPD.txt –
  • taxasummary.txt



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