Changelog

1.1.alpha19

• Closed GH-352: Showing percent identity in the CSV file.

1.1.alpha18

• Closed GH-346: Adding proper support for ambigious amino acid codes.

1.1.alpha17

• Closed GH-340: “malformed row in jplace” after pplacer warning “computed function value is infinite or NaN”.
• Closed GH-339: Better error message concerning strange mass.

1.1.alpha16

• Closed GH-334: multiclass_concat.py modifies placement database such that classif_table.py returns accurate tallies.

1.1.alpha15

• Closed GH-320: Now compiles fine with Batteries 2.
• Closed GH-327: Ignore sequences that aren’t in both jplace and sequence files.
• Closed GH-312: An improved script for managing classification results, called classif_table.py; classif_rect.py is now deprecated.
• Closed GH-315: support rppr info on reference packages lacking a taxonomy
• Closed GH-316: pplacer warns rather than fails when an alignment looks like nucleotides
• Closed GH-317: pplacer --write-masked-out respects --out-dir
• Closed GH-318: Apply alignment mask on a per-placement basis
• Closed GH-319: pplacer --write-pre-masked no longer exits after writing mask.
• Closed GH-322: Moved to Batteries version 2.1.0. Supports OCaml 4.01.0
• Closed GH-323: pplacer, guppy, and rppr support gzip-compressed alignment and .jplace files.
• Closed GH-324: deduplicate_sequences.py supports gzip-compressed FASTA files.

1.1.alpha14

• Closed GH-181: Added guppy indep_c; added --leaf-values to guppy mft.
• Closed GH-215: Added pca_for_qiime.py and extract_taxonomy_from_biom.py; changed guppy and rppr to allow BIOM files to be passed as arguments where placefiles are allowed.
• Closed GH-241: On the NBC classifier of guppy classify: renamed --target-rank to --nbc-rank; added --nbc-rank auto.
• Closed GH-248: Added premasking by default to the NBC classifier of guppy classify; correspondingly added --no-pre-mask.
• Closed GH-250: Completely revamped classification.
• Closed GH-251: Added the hybrid5 classifier.
• Closed GH-256: Added --mmap-file to pplacer; changed --pretend in pplacer to show the amount of memory which would be allocated.
• Closed GH-259: Added guppy mcl and a --mcl flag to guppy compress.
• Closed GH-260: Added rooted_pd to guppy fpd; Added a --variance flag to guppy rarefact.
• Closed GH-261: Added rppr convex_taxids.
• Closed GH-262: Added --as-mass to guppy redup; updated sort_placefile.py for the new placefile format; fixed pplacer to better deal with internal edges on a tree with a branch length of 0.
• Closed GH-263: Fixed a bug that could sometimes cause failures in rppr min_adcl with the PAM algorithm.
• Closed GH-265: Fixed a bug that could cometimes cause rppr reroot to return a suboptimal rooting.
• Closed GH-266: Adding map_ratio and map_overlap columns to guppy to_csv.
• Closed GH-267: Added a leaf_count column to rppr convex_taxids.
• Closed GH-268: Merged various minor fixes.
• Closed GH-273: Fix convexify for multifurcating trees
• Closed GH-274: Added --weight-as-count to guppy rarefact.
• Closed GH-276: Added -k to guppy rarefact.
• Closed GH-277: Added --weight-as-count to guppy rarefy.
• Closed GH-278: Changed guppy rarefact to allow multiple placefiles to be passed instead of just one.
• Closed GH-282: Added a --inflation flag to guppy mcl and guppy compress.
• Closed GH-286: Changed pplacer’s --mmap-file to accept a path to either a directory or a file.
• Closed GH-287: Added a more informative error message for the case of an input alignment containing some, but not all reference sequence names.
• Closed GH-288: Added guppy placemat
• Closed GH-290: Random tie breaking in NBC classifier
• Closed GH-291: Added qD(T) alpha diversity measure from Chao et. al., 2010 (doi:10.1098/rstb.2010.0272)
• Closed GH-293: Switched build system to use OPAM
• Closed GH-294: Added --unitize option to guppy squash
• Closed GH-297: Support multiprocessing during squash cluster bootstrapping
• Closed GH-298: Faster upper-limit finding during integration
• Closed GH-299: Fix NaN likelihoods for empirical frequencies + unseen state
• Closed GH-303: Updated Batteries dependency to version 2.0.0
• Closed GH-305: Eliminate compilation warnings from CDD
• Closed GH-306: Random tie breaking is default in NBC
• Closed GH-307: Renamed --kappa to --theta, awpd to bwpd in guppy fpd
• Closed GH-309: Support overlap minimization (SOM) added to guppy epca (see also GH-221)

1.1.alpha13

• Fixed a bug where pplacer would sometimes fail abruptly with a Child_error of EBADF on close(2). [rc2]
• Added missing -o and related flags to guppy to_csv. [rc3]
• Fixed minor errors in the documentation [r2]
• Closed GH-216: Added guppy trim and guppy check.
• Closed GH-225: Added rppr vorotree.
• Closed GH-235: Added --rep-edges flag for the splitify subcommands.
• Closed GH-237: Added a multiplicity column to guppy diplac.
• Closed GH-238: Added --epsilon for splitify commands to filter constant edges out of the resulting splitify matrices.
• Closed GH-239: Added the pam algorithm to voronoi commands; cleaned up voronoi full algorithm and implementation.
• Closed GH-240: Added a -o flag for pplacer.
• Closed GH-242: Renamed ECLD to ADCL; added –max-adcl to voronoi commands.
• Closed GH-243: Updated rppr reroot so it can run on reference packages which have unannotated sequences.
• Closed GH-244: Updated rppr infer to handle sequences which could not be reasonably placed anywhere on the tree.
• Closed GH-245: Updated code to allow refpkgs to be passed as .zip files as well as directories.
• Closed GH-246: Added –always-include to voronoi commands.
• Closed GH-247: Added guppy unifrac.
• Closed GH-249: Added guppy rarefy.
• Closed GH-252: Added --all-alternates to rppr convexify.
• Closed GH-253: Added --no-collapse to guppy diplac.
• Closed GH-255: Added guppy to_csv.
• Closed GH-257: Renamed rppr voronoi to rppr min_adcl, rppr vorotree to rppr min_adcl_tree, and guppy diplac to guppy adcl. Added --seed to rppr min_adcl and rppr min_adcl_tree.
• Closed GH-280: Fixed a bug in which pplacer would fail if passed -t and -s flags without also passing a -c or -r flag.

1.1.alpha12

• Added guppy to_rdp and guppy classify_rdp.
• Closed GH-113: Updated the best_classification and multiclass SQL views; correspondingly changed the flags to rppr prep_db; added the placement_evidence table for bayes classification.
• Closed GH-183: Added documentation for more functions.
• Closed GH-189: Added guppy pentropy.
• Closed GH-191: Added -m to guppy redup; bumped the jplace format version to 3 with the ability to give each name for a pquery a different mass.
• Closed GH-192: Added rppr infer.
• Closed GH-193: Added rppr reclass.
• Closed GH-194: Added a mass column to placement_names to parallel new features in the jplace format.
• Closed GH-195: Added a –groups flag to pplacer for placing metagenomic sequences onto trees built from very wide alignments.
• Closed GH-196: Added code to pplacer to better handle errors raised when calling fork(2).
• Closed GH-198: Added progress reporting code to guppy compress.
• Closed GH-199: Renamed guppy pentropy to guppy entropy; added quadratic entropy calculation.
• Closed GH-200: Added –discard-below to guppy {islands,compress}.
• Closed GH-201: Added a setup.py file to the scripts directory.
• Closed GH-202: Added rppr prepsim; added –include-pendant to guppy diplac.
• Closed GH-204: Added more columns to rppr reclass.
• Closed GH-205: Added guppy error.
• Closed GH-206: Updated some pplacer documentation.
• Closed GH-207: Added CSV output to guppy edpl.
• Closed GH-208: Fixed the -o flag to reflect the actual file written to for guppy {sing,tog,edpl}.
• Closed GH-209: Fixed a bug preventing Gcat_model refinement if the supplied alignment had a different number of sites from the refpkg; added –always-refine to pplacer.
• Closed GH-210: Merged guppy {pd,wpd,entropy} into guppy fpd.
• Closed GH-212: Changed parsing error messages to be more specific.
• Closed GH-213: Added PyNAST support to refpkg_align.py.
• Closed GH-214: Added guppy ograph.
• Closed GH-218: Added –split-csv to guppy merge.
• Closed GH-219: Fixed some guppy commands which needed a zero root branch length.
• Closed GH-220: Added error messages for some exceptions; fixed guppy rarefact.
• Closed GH-222: Added a -c flag to guppy bary.
• Closed GH-236: Fixed support for numeric leaf names when writing out XML.

1.1.alpha11

• Fixed a bug with parsing MAP identity from a jplace file.
• Fixed a bug that occurred sometimes when running rppr convexify on a tree where not every leaf had a corresponding tax_id at a particular rank.
• Fixed a bug with fasttree placements which caused failure when the site categories had to be calculated (ie. when using a combined reference + query alignment)
• Changed versions to be parsed only out of git tags.
• Closed GH-42: Added –edpl flag to guppy fat for EDPL coloring in fat trees.
• Closed GH-146: Added an –unweighted flag to guppy pca.
• Closed GH-168: Changed guppy and rppr to list the subcommands in –help; reformatted the options flags to be more readable.
• Closed GH-169: Fixed all commands that work on reference packages to use the -c flag to specify the reference package.
• Closed GH-176: Fixed rppr reroot to handle cases where not all tax_ids are specified under the rank the rerooting is happening at.
• Closed GH-177: Added –mass-gt and –mass-le flags to guppy filter.
• Closed GH-178: Fixed guppy compress to add a zero root branch length.
• Closed GH-179: Changed the JSON emitter to be able to represent a wider range of floats.
• Closed GH-182: Changed ‘weighted’ to ‘spread’ and ‘unweighted’ to ‘point’ across all the guppy and rppr commands.
• Closed GH-184: Added a placement_median_identites table for guppy classify.
• Closed GH-188: Added support for a reference package to be able to specify that some reference sequences are unclassified.

1.1.alpha10

• Closed GH-126: Split Glv/Model into Gmix_model and Gcat_model with the option of adding more models to pplacer later.
• Closed GH-154: Added guppy islands.
• Closed GH-156: Added functionality for calculating multiple KR distances with only one tree traversal.
• Closed GH-157: Added guppy compress.
• Closed GH-162: Added fig ranking to pplacer.
• Closed GH-163: Added a –node-numbers flag to every command that emits a phyloxml tree which adds the tree’s node numbers to the phyloxml output as bootstrap values.
• Closed GH-172: Switched from using xml-light to xmlm.

1.1.alpha09

• Fixed a bug that was making classifications appear too specific when the placement was on the edge just proximal to an MRCA.
• Fixed a bug wherein the Newick parser would add a ‘.’ to the end of leaf names if the name was an integer.
• In fixing a bug, made guppy diplac only emit the first name in a pquery in its results.
• Fixed a bug that caused the trailing } in a JSON file to be omitted when the file was large enough.
• Added a multiclass view and associated parameters to rppr prep_db.
• Fixed a bug where sometimes placements that fell too close to the root would vanish with the –map-identity flag on.
• Fixed identity to give 0% sequence identity in the case of no overlap between sequences.
• Fixed a bug by flushing all output buffers before forking, so that the same data isn’t written multiple times.
• Fixed a bug in pplacer in which it wouldn’t write the original reference tree when creating a placefile.
• Fixed some issues with phyloxml generation.
• Closed GH-27: Reorganized functions that operate on alignments.
• Closed GH-67: Added guppy wpd.
• Closed GH-72: Added new features to rppr convexify and fixed the implementation of the convexify algorithm, as it cut too many leaves in some corner cases.
• Closed GH-75: Changed mass maps to use records types instead of tuples.
• Closed GH-76: Added a check in guppy classify to ensure that the sqlite database has been properly initialized.
• Closed GH-78: Added an –average flag to guppy fat.
• Closed GH-81: Removed old code that was deprecated by batteries; changed most code to be using batteries.
• Closed GH-82: Merged the pick branch into dev.
• Closed GH-84: Renamed .json to .jplace for new-format placefiles.
• Closed GH-85: Added better error messages for potential premasking failures.
• Closed GH-86: Dropped support for older versions of the reference package format.
• Closed GH-88: Improved handling very small alphas in pplacer, working around a problem with the GSL that wasn’t allowing us to invert the CDF for the gamma distribution.
• Closed GH-89: Fixed some bugs in the convexify algorithm.
• Closed GH-90: Added an error message for if pplacer is invoked with no arguments.
• Closed GH-91: Added more documentation to .mli files.
• Closed GH-92: Added searching and alignment scripts.
• Closed GH-94: Improved the leaf selection criteria in rppr voronoi.
• Closed GH-96: Now using colors from colorbrewer2.org for heat.
• Closed GH-98: Added a –map-identity flag to pplacer.
• Closed GH-99: Added more examples for guppy batchfiles.
• Closed GH-101: Added virtual placefiles to guppy batchfiles.
• Closed GH-103: Added batteries as a dependency.
• Closed GH-104: Added a naive reference implementation of convexify, accessible with a –naive flag.
• Closed GH-105: Added parameter substitution to guppy batchfiles.
• Closed GH-108: Added more data from jplace files into the taxtable schema; added a way to change the cutoff for best_classifications.
• Closed GH-109: Added a rppr info subcommand.
• Closed GH-110: Added a –no-early flag to rppr convexify.
• Closed GH-111: Added a script to update reference packages to version 1.1.
• Closed GH-112: Improved some of pplacer’s error messages.
• Closed GH-114: Changed MAP identity in placefiles to be stored flat instead of nested.
• Closed GH-115: Updated the documentation to reflect changes to the SQL schema in rppr prep_db.
• Closed GH-116: Added –keep-at-most and –keep-factor flags to pplacer.
• Closed GH-117: Added the output of git describe to –version output.
• Closed Gh-118: Added a –quiet flag to guppy and rppr.
• Closed GH-119: Added a rppr reroot subcommand.
• Closed GH-120: Added a –rank-limit flag to rppr convexify.
• Closed GH-122: Renamed rppr taxtable to rppr prep_db.
• Closed GH-124: Rewrote the Newick parser.
• Closed GH-125: Added a –rooted flag to rppr convexify.
• Closed GH-128: Added informative priors to pplacer integration.
• Closed GH-129: Added the ability for rppr convexify to convexify a tree not in a reference package.
• Closed GH-130: Added guppy pd.
• Closed GH-131: Changed pplacer to set some defaults with the -p flag.
• Closed GH-133: Added edge painting classification by default to pplacer and a corresponding –painted flag to rppr ref_tree.
• Re-closed GH-133: Added checks for the case when not all ranks are represented by some sequence in the reference package.
• Closed GH-135: Generally improved error messages in pplacer, guppy, and rppr.
• Closed GH-138: Removed the –transform flag from everything except guppy mft; removed the –unweighted flag from commands which don’t respect it.
• Closed GH-139: Added a check to pplacer to ensure all query sequences have at least some overlap with some reference sequence.
• Closed GH-140: Allowed pplacer to be run with -t and without -r or -c.
• Closed GH-141: Removed compare_placements.py; added check_placements.py; documented the rest of the python scripts.
• Closed GH-143: Changed the –leaves argument to rppr voronoi to specify the number of leaves to keep in the tree instead of the number of leaves to prune.
• Closed GH-144: Changed pplacer to explicitly disallow unplaced sequences from being written out; changed best_classifications and multiclass views to yield NULL for rows where no placements match all the criteria.
• Closed GH-149: Updated the jplace version to 2; changed the Newick parser and emitter to allow for the new format of trees with edge numbers specified in braces instead of brackets.
• Closed GH-153: Changed guppy mft to not squash name lists to mass by default.
• Closed GH-155: Changed pplacer to always check for invalid bases when pre-masking sequences.
• Closed GH-159: Updated to use the v2 batteries API.
• Closed GH-164: Fixed some bugs related to various APIs not knowing how to deal with node labels on non-leaves.
• Closed GH-167: Fixed an issue where rppr reroot wasn’t updating the bark of trees correctly.

1.1.alpha08

• Closed GH-46: Added a –timing flag to pplacer to show where time was spent during placements.
• Closed GH-47: Added unit tests for gaussian kr distance.
• Closed GH-49: Added a more informative error message to pplacer if reference sequences occur multiple times in a query file.
• Closed GH-52: Fixed padding in guppy squash.
• Closed GH-58: Improved navigation for the documentation on guppy commands.
• Closed GH-59: Improved documentation for guppy commands using sqlite.
• Closed GH-60: Improved documentation for guppy classify.
• Closed GH-65: Released alpha08.
• Closed GH-66: Added a FAQ to the documentation.
• Closed GH-68: Changed guppy info to show multiplicity.
• Closed GH-69: Changed guppy tog to use polytomy instead of a _ delimiter joining sequence names.
• Closed GH-70: Added documentation for how to compile pplacer.
• Closed GH-73: Added a pre-masking feature to cut out irrelevant columns of the alignment.
• Closed GH-74: Improved how pplacer dedupes sequences before a placerun.
• Added a script to sort placefiles for easier visual diffs.
• Added more informative error messages when the length of the query alignment and reference alignment don’t match.
• guppy edpl now calculates the EDPL (expected distance between placement locations) for placements

1.1.alpha07

• Fixed a serious issue with any command that used a --prefix flag.

1.1.alpha06

• Closed GH-20: efficiency of kr_distance evaluated and approved.
• Closed GH-44: improved sqlite3 support in guppy.
• Closed GH-45: better consistency of output flags across all guppy commands.
• Closed GH-48: better error reporting when loading json placefiles.
• Closed GH-50: fixed the output of guppy classify.
• Closed GH-51: only parsing the first word as a sequence name in a fasta file.
• Renamed the --normal flag for guppy kr to --gaussian to avoid confusion with normalization.
• Only one shuffle at a time is now stored in memory (big savings, obviously).
• Fixed bug that was throwing off guppy kr shuffling significance estimation.
• guppy pca now defaults to scaling eigenvalues to percent variance; now has a –raw-eval flag to specify otherwise.
• Fixed all of the sequence parsers to be tail-recursive, so parsing large files no longer causes segfaults.
• Added a guppy redup command for re-adding duplicate sequences to placefiles generated from deduplicated sequence files.

1.1.alpha05

• Closed GH-11: options for the tree-generating subcommands are more uniform.
• Closed GH-22: added more unit tests for guppy kr.
• Closed GH-32: using power iteration rather than full eigendecomposition. Leads to 60x speedup for PCA on demo data.
• Closed GH-35: added a remark in the documentation about multiple comparison.
• Closed GH-41: added docs for the json placefile format.
• Added guppy splitify. Spits out differences of mass across splits.
• Changed default behavior of guppy kr to not normalize, and correspondingly added in a --normalize command line flag.
• Improved documentation.
• Moved guppy heat to guppy kr_heat.
• The guppy heat subcommand now maps an arbitrary vector to a phylogenetic tree contained in a reference package.
• Removed redundant classic subcommand from guppy.
• Changed guppy round to use the new placefile format.
• Added support for posterior probabilities in json placefiles.
• Removed csv and old-placefile-format generation from pplacer.
• Added the ability to run pplacer in multiple processes in parallel with the -j flag.
• Removed friend-finding from pplacer, as it was superseded by some of the multiprocessing code.

1.1.alpha03 to 1.1.alpha04

• Closed GH-12: removed Placement.classif, and renamed Placement.contain_classif to Placement.classif.

• Closed GH-29: added guppy merge to merge multiple placefiles.

• Closed GH-30: accepting r, n, and rn as delimiters everywhere in pplacer and guppy.

• Closed GH-36: added guppy {classic,tog,sing,filter}. The former three were originally a part of placeviz, and the lattermost filters placefiles to only a specific subset of their placements.

• Closed GH-37: added a trailing newline to the end of json files.

• Closed GH-38: added this changelog.

• Bugfix in guppy classify. From the commit:

  Previously, a file was being opened and closed for every pquery in every placerun. This resulted in only the last pquery being classified and written out. Now only one file is being opened for each placerun.