Mashtree - v1.4.6

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 2 years ago

Mashtree - v1.4.3

Bump the latest release

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 3 years ago

Mashtree - v1.4.0

Removed the SQLite requirement. Now uses a TSV backend. I am labeling this as a pre-release because although it has passed my own unit tests, I need to give time to the community to give feedback.

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 3 years ago

Mashtree - Fixed bootstrap bug

• Bootstrap bug (see: #66)
• Unit testing

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 3 years ago

Mashtree - pseudophylogeny

This is a test to look into a pseudophylogenetic method, where presence/absence of hashes is used in a binary alignment. This alignment is given to raxml to make a maximum likelihood interpretation for a tree.

This is in alpha and not tested at all. Use at your own risk. (but feedback is always welcome!)

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 5 years ago

Mashtree - v1.2.0

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 5 years ago

Mashtree - v1.0.4

• Fixed --citation
• Removed a perl module dependency

Thank you @kapsakcj for finding all these recent documentation issues and installation warnings

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 6 years ago

Mashtree - v1.0.2

Fixed yet one more installation warning

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 6 years ago

Mashtree - v1.0.1

Fixed an installation warning on bioperl

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 6 years ago

Mashtree - v1.0

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 6 years ago

Mashtree - v0.57

• Transfer bootstrap expectation
• More documentation on bootstrapping
• Some stabilizing fixes

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 7 years ago

Mashtree - Fixed bootstrapping

There was a bug where the new seed was not being applied to each mashtree iteration

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 7 years ago

Mashtree - Fixed the cpan installation

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 7 years ago

Mashtree - v0.50

Fixed a bug with adding distances to the database

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 7 years ago

Mashtree - v0.41

Fixed some unit test bugs from v0.40. Addresses #37

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 7 years ago

Mashtree - v0.40

Jack knifing enabled! Make trees with confidence.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 7 years ago

Mashtree - v0.37

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 7 years ago

Mashtree - accurate mode is better

• Fixed a bug with multithreaded accurate mode (--min-depth 0) and bumped the version up so that cpan could catch it.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 7 years ago

Mashtree - v0.35.1

• Changed the minimum abundance finder algorithm a little
• --outtree now an option
• Fixed the bug where multithreading caused a segfault
• Fixed a race condition bug

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 7 years ago

Mashtree - v0.34

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 7 years ago

Mashtree - v0.33

Fixed distance matrix bug

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 8 years ago

Mashtree - v0.32

• The mashtree executable is now mashtree instead of mashtree.pl
• Quicktree is now required
• Increased precision of distances between genomes
• added mashtree module to testing environment
• Fixed some warnings related to the minimum abundance finder
• Fixed the findDistances bug by updating the SQL queries

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 8 years ago

Mashtree - Mashtree v0.29

• better documentation on cpan (?)
• mashtree instead of mashtree.pl
  • I'll have a deprecation message for several versions, until we are comfortable removing mashtree.pl
• treeDist() method to describe a distance between two trees

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.28

• Updated the unit tests so that they work with QuickTree too.
• Created a tree distance metric to help with the unit tests.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - 0.27

Same as 0.27a except I remembered to add the correct version number. Sorry for the confusion.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - 0.27a

• SQLite woes are probably fixed. No longer are we capped at 1000 genomes. Thank you @fbristow for the pull request. Thanks to everyone else for bringing it to my attention.
• Added test to make sure the database is working properly (t/10_sqlite.t)
• QuickTree is now an option. If it is in your PATH then it will use QuickTree which produces the same tree but faster.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.26

For the minimum abundance filter (--min-depth 0), using Mash for generating a histogram. Thanks for the tip @boydgreenfield.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.25

Some metadata for CPAN was fixed.

Chunking insert statements so as to not overload sqlite. See issue #11 .

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.23

More minor fixes

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.22

This version isn't a huge update. Just minor changes.

• Cleaning up intermediate files better
• Native reading of fastq.gz files into Mash. Hopefully that speeds things up a bit.

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 8 years ago

Mashtree - v0.21

Mash files (.msh) can now be used as input.

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 9 years ago

Mashtree - v0.20

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 9 years ago

Mashtree - v0.16

• Removed Thread::Queue in favor of arrays. Hopefully not locking other threads will make large-threaded runs run faster (e.g., --numcpus 100). It seems to trim off a second on some trial runs, so it is might be doing the job but not necessarily a huge decrease.
• --version is easier to parse from other programs
• Fixed random bugs having to do with .gbk.gz inputs
• v0.15 is on CPAN and is almost the same as this version except --version

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 9 years ago

Mashtree - v0.14

• Optimized adding distance to the database some more. Seems to have shaved off half a second on my 85-genome assemblies test set with 32 or 64 threads.
• Added --version. It is also shown in the documentation but not yet in README.md.
• Made compatible with CPAN and Travis CI. This includes unit tests. So far v0.12 is in CPAN.
• Checking for files of the same basename in case multiple input directories are involved.

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 9 years ago

Mashtree - v0.12 - with unit testing

• Conforms better to the standard Perl project format
  • The user is now responsible for installing bioperl and any other perl modules
  • t/ directory with test data now present
  • make test instead of make check
• I figured out how to use travis-ci for unit testing. Ready for any pull requests!
• Minor changes to README.md

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 9 years ago

Mashtree - v0.11 - richseq and compressed files now welcome

• Richseq files - gbk, embl, and swissprot are now accepted
• Compressed files - .gz, .bz2, and .zip are now accepted.

These changes have not been tested, hence the pre-release tag.

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 9 years ago

Mashtree - v0.10

• GenBank, EMBL, and SwissProt support for genome assemblies
• Extra cpus are not wasted as much: Mash will be run with multiple threads if extra cpus are given with --numcpus.
• Refactored the minimum abundance filter and added KMC support. However, KMC does not seem to be as accurate for detecting peaks and valleys in kmer frequencies.

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 9 years ago

Mashtree - v0.09

• Fixed the minimum abundance filter bug where it was not triggered with a depth of 0
• Added onto the Makefile for checking prerequisite software
• Output distance matrix is now a well-defined flag in both mashtree.pl and mashtree_wrapper.pl instead of a hidden feature
• Updated documentation

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 9 years ago

Mashtree - v0.08 - the database edition

• SQLite added
• Readme.md and Makefile reflect new SQLite addition
• SQLite is a prerequisite now
• Multithreaded mashtree_wrapper.pl

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 9 years ago

Mashtree - v0.07

• more multithreading
• jellyfish is used if present for the minimum abundance filter, if it's present

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 9 years ago

Mashtree - v0.06 - refactored

• Fixed a bug with the min kmer filter
• Removed some instances where caching temporary files got in the way
• Added a version statement in the usage
• Refactored mashtree_wrapper.pl
• Updated README.md

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 9 years ago

Mashtree - v0.05 - abundance filter

• Added a new abundance filter that searches for kmer "valleys"
• Enable this filter by specifying --mindepth 0 when using fastq files
• idea from Alex Jironkin and Anthony Underwood, but I created a version that is unfortunately not as fast but does not require any additional dependencies.
  • https://bitsandbugs.org/2016/07/29/mash-and-khmer-abundance/

Scientific Software - Peer-reviewed - Perl
Published by lskatz over 9 years ago

Mashtree - v0.04

• Sketch size is now an option
• Bootstrapping is done based on input order and neighbor-joining. Thanks to Jo Williams for that idea.
• Slightly better documentation

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 10 years ago

Mashtree - v0.03

I refactored the code - bin directory - wrapper script for running the instances of mashtree.pl in case of bootstrapping - Mashtree.pm module to help abstract some things

I also validated: - The tree of 524 genome assemblies from v0.03 looks like the same from an older version

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 10 years ago

Mashtree - v0.02

• added methods to add assemblies into the mash tree
• Refined raw reads parameters in sketches

Scientific Software - Peer-reviewed - Perl
Published by lskatz almost 10 years ago

Mashtree - Seems to be working with multithreads

Scientific Software - Peer-reviewed - Perl
Published by lskatz about 10 years ago