Package: shiptv
Standalone HTML Interactive Phylogenetic Tree VizGenerate a standalone HTML file with an interactive phylogenetic tree usingPhyloCanvasFree software: Apache Software License 2.0Documentation:https://shiptv.readthedocs.io.See test shiptv HTML output here:fmdv-5-shiptv.htmlPhylogenetic tree of 5 FMDV genomesPhylogenetic tree of IAV HA gene sequencesFeaturesInteractively view your tree in the browser with metadata highlighted beside your tree using PhyloCanvas.Visualize your own metadata! Provide a tab-delimited table as input with--metadatayour-metadata-table.tsvSelect metadata fields to display beside phylogenetic tree with select boxAutomatically retrieve metadata from a GenBank file!Highlight branches with low support in the browser.Collapse branches with low support (e.g.-C95for IQ-TREE trees with UFBoot-bb1000to collapse branches with less than 95% support).Toggle full window mode withshift+ctrl+f. Works well with F11 fullscreen mode.UsageShow help info:$ shiptv --helpInstall shiptv completions for current shell:$ shiptv --install-completionMost basic usage would be to create a tree from a Newick format tree file:$ shiptv -n newick.treefile -o shiptv-tree.htmlMore advanced usage would be to provide a tab-delimited table of metadata with the first field containing sample names identical to those in the Newick tree file:$ shiptv -n newick.treefile --metadata my-metadata.tsv -o shiptv-tree.htmlWith a reference sequence Genbank fileref.gb, a Newick format phylogenetic treetree.nwk, output atree.htmlstandalone HTML interactive phylogenetic tree visualization and ametadata-table.tsvtab-delimited table of metadata fromref.gb.shiptv-rref.gb-ntree.nwk-otree.html-mmetadata-table.tsvHelp output$ shiptv --help
Usage: shiptv [OPTIONS]

  Create HTML tree visualization with metadata.

  The metadata for reference genomes can be extracted from the specified
  Genbank file.

  Any leaf names that are present in the tree but not present in the Genbank
  file are assumed to be user samples and are flagged as such in the
  metadata table as "user_sample"="Yes".

Options:
  -n, --newick PATH               Phylogenetic tree Newick file  [required]
  -o, --output-html PATH          Output HTML tree path  [required]
  -N, --output-newick PATH        Output Newick file
  -r, --ref-genomes-genbank PATH  Reference genome sequences Genbank file
  -m, --output-metadata-table PATH
                                  Output metadata table path
  --leaflist PATH                 Optional leaf names to select from
                                  phylogenetic tree for pruned tree
                                  visualization. One leaf name per line.

  --genbank-metadata-fields PATH  Optional fields to extract from Genbank
                                  source metadata. One field per line.

  -M, --metadata PATH             Optional tab-delimited metadata for user
                                  samples to join with metadata derived from
                                  reference genome sequences Genbank file.
                                  Sample IDs must be in the first column.

  --metadata-fields-in-order PATH
                                  Optional list of fields in order to output
                                  in metadata table and HTML tree
                                  visualization. One field per line.

  --fix-metadata / --no-fix-metadata
                                  Try to automatically fix metadata from
                                  reference Genbank file.  [default: True]

  -C, --collapse-support FLOAT    Collapse internal branches below specified
                                  bootstrap support value (default -1 for no
                                  collapsing)  [default: -1.0]

  --highlight-user-samples / --no-highlight-user-samples
                                  Highlight user samples with metadata field
                                  in tree.  [default: False]

  --outgroup TEXT                 Tree outgroup taxa
  --midpoint-root / --no-midpoint-root
                                  Set midpoint root  [default: False]
  --verbose / --no-verbose        Verbose logs  [default: False]
  --install-completion            Install completion for the current shell.
  --show-completion               Show completion for the current shell, to
                                  copy it or customize the installation.

  --help                          Show this message and exit.CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.4.1 (2021-05-13)ensure tree rendered even ifgenomeMetadataobject is empty inphylocanvas.htmladd--versionoption to print shiptv version and exitadd epilog to help with version infoadd example usage to helpchange--metadatashort opt to-mfrom-Mchange--output-metadata-tableshort opt from-mto-Mupdate lodash JS library to version 4.17.150.4.0 (2021-02-12)Add Select2 metadata field select box to show metadata fields in the order requiredAdd Shift+Ctrl+F to toggle tree viz full window modeUsing BioPython’s Phylo module for phylogenetic tree manipulation. Removed ete3.Using Requests library to get JS and CSS to embed into HTML outputMigrated to Typer from Click for CLIAdded Rich for nicer logging and tracebacksChanged some options to be optional; only required options are-n/--newickand-o/--output-htmlBy default don’t highlight user samples as a field of metadata in tree vizAllow user to optionally specify outgroup taxa nameAllow user to optionally re-root tree at midpoint nodeFixed warnings from Pandas when modifying view of dataframe by using.loc[]Moved to GitHub Actions CI and PyPI deployment0.3.0 (2019-10-02)Fix rendering of numeric and ISO date metadata fieldsReference genomes Genbank now optionalUpdated docs0.2.0 (2019-06-28)Added low support branch highlighting in tree HTML fileAdded option to collapse low support branches (-C/–collapse-support)Added option to output modified Newick tree file (-N/–output-newick)Fixed date/time parsing from Genbank files (#1)0.1.0 (2019-05-10)First release on PyPI.