Ecosyste.ms: Issues

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GitHub / biocore/horizomer issues and pull requests

#80 - walk_copy, root_above and their unit tests added

Pull Request - State: closed - Opened by iiiime over 6 years ago

#79 - compare_branch_lengths function and its unit tests added

Pull Request - State: closed - Opened by iiiime over 6 years ago - 3 comments

#78 - added some doctests

Pull Request - State: closed - Opened by qiyunzhu over 6 years ago - 1 comment

#77 - function cladistic and its unit test added

Pull Request - State: closed - Opened by iiiime over 6 years ago - 1 comment

#76 - Utils

Pull Request - State: closed - Opened by iiiime over 6 years ago - 3 comments

#75 - added collapsing functions

Pull Request - State: closed - Opened by qiyunzhu almost 7 years ago - 4 comments

#74 - added intersecting trees function

Pull Request - State: closed - Opened by qiyunzhu almost 7 years ago - 2 comments

#73 - build tree of genome set based on NCBI taxonomy

Pull Request - State: closed - Opened by qiyunzhu almost 7 years ago - 9 comments

#72 - Updated way to call scikit-bio IntervalMetadata

Pull Request - State: closed - Opened by qiyunzhu over 7 years ago

#71 - (WIP) Installation guide for Debian / Ubuntu users

Issue - State: open - Opened by qiyunzhu over 7 years ago

#70 - fixed bug for PhyloPhlAn wrapper

Pull Request - State: closed - Opened by qiyunzhu over 7 years ago - 2 comments

#69 - Codebase reorganization step 1 - renaming

Pull Request - State: closed - Opened by qiyunzhu over 7 years ago - 1 comment

#68 - (WIP) Re-organize the codebase

Issue - State: open - Opened by qiyunzhu over 7 years ago

#67 - moving prototype selection

Pull Request - State: closed - Opened by sjanssen2 over 7 years ago - 1 comment

#66 - support for 'seedsets' in destructive_maxdist heuristic:

Pull Request - State: closed - Opened by sjanssen2 over 7 years ago - 14 comments

#65 - added include function to prototype selection

Pull Request - State: closed - Opened by qiyunzhu over 7 years ago - 5 comments

#64 - Mac's readlink compatibility

Issue - State: open - Opened by qiyunzhu over 7 years ago - 1 comment

#63 - added write sampled genes function

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 4 comments

#62 - added sample genes script

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 9 comments

#61 - refreshed orthofinder support to latest generic version

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 11 comments

#60 - added taxon sampling script

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 6 comments

#59 - DarkHorse2 automated installation script

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 12 comments

#58 - Added Phylomizer runner

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 8 comments

#57 - Added installation instructions

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 13 comments

#56 - added script for running phylophlan

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 12 comments

#55 - modularize Bash scripts

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 7 comments

#54 - updated launch_benchmark

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 4 comments

#53 - [WIP] improvement in Bash scripts

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 4 comments

#52 - [WIP] updated dependency

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 6 comments

#51 - after code review clean-up (done)

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 4 comments

#50 - add darkhorse call for candidate genomes

Pull Request - State: closed - Opened by ekopylova almost 8 years ago - 3 comments

#49 - scikit-bio version description

Pull Request - State: closed - Opened by qiyunzhu almost 8 years ago - 1 comment

#48 - Issue 23

Pull Request - State: closed - Opened by ekopylova almost 8 years ago

#47 - Prototype selection destructive maxdist

Pull Request - State: closed - Opened by sjanssen2 about 8 years ago - 8 comments

#46 - added another heuristic for prototype selection, based on the p-media…

Pull Request - State: closed - Opened by sjanssen2 about 8 years ago - 5 comments

#45 - edited Bash scripts for EGID and GeneMark

Pull Request - State: closed - Opened by qiyunzhu about 8 years ago - 5 comments

#44 - Updated GenBank parser based on latest scikit-bio dev

Pull Request - State: closed - Opened by qiyunzhu about 8 years ago - 12 comments

#43 - Merge parse_output and added parse Genemark

Pull Request - State: closed - Opened by qiyunzhu about 8 years ago - 8 comments

#42 - Need to update GenBank parser once scikit-bio is updated

Issue - State: closed - Opened by qiyunzhu about 8 years ago

#41 - Merged reformat_input_gi into reformat_input

Pull Request - State: closed - Opened by qiyunzhu about 8 years ago - 20 comments

#40 - simulate_hgts.py adds GenBank output

Pull Request - State: closed - Opened by qiyunzhu about 8 years ago - 3 comments

#39 - add darkhorse parser and candidate genomes output

Pull Request - State: closed - Opened by ekopylova about 8 years ago

#38 - Add GenBank output for simulated HGTs

Issue - State: open - Opened by ekopylova about 8 years ago

#37 - Test distance matrices for prototype selection problem

Pull Request - State: open - Opened by ekopylova about 8 years ago - 1 comment

#36 - Prototype selection constructive protoclass

Pull Request - State: closed - Opened by sjanssen2 about 8 years ago - 10 comments

#35 - Adding coveragerc

Pull Request - State: closed - Opened by josenavas about 8 years ago - 4 comments

#34 - added a heuristic function to select prototypes.

Pull Request - State: closed - Opened by sjanssen2 about 8 years ago - 12 comments

#33 - Conda recipe for PhyloNet

Issue - State: open - Opened by ekopylova about 8 years ago

#32 - Prototype selection exhaustive

Pull Request - State: closed - Opened by sjanssen2 about 8 years ago - 15 comments

#31 - update egid

Pull Request - State: closed - Opened by qiyunzhu over 8 years ago - 13 comments

#30 - run HGTector and parse output

Pull Request - State: closed - Opened by qiyunzhu over 8 years ago - 16 comments

#29 - setup code for data preprocessing with Phylomizer and DarkHorse parsing

Pull Request - State: closed - Opened by ekopylova over 8 years ago - 7 comments

#28 - Conda recipe for MUSCLE

Issue - State: open - Opened by ekopylova over 8 years ago

#27 - Conda recipe for KALIGN

Issue - State: open - Opened by ekopylova over 8 years ago

#26 - Conda recipe for Jane4

Issue - State: open - Opened by ekopylova over 8 years ago

#25 - Conda recipe for Ranger-DTL

Issue - State: open - Opened by ekopylova over 8 years ago

#24 - Merge putative HGTs into summary

Issue - State: open - Opened by ekopylova over 8 years ago

#23 - parse HGTs from DarkHorse output

Issue - State: open - Opened by ekopylova over 8 years ago

#22 - update scikit-bio channel to biocore for GenBank parser

Issue - State: closed - Opened by ekopylova over 8 years ago - 1 comment

#21 - issue 19

Pull Request - State: closed - Opened by ekopylova almost 9 years ago - 6 comments

#20 - add compositional tools

Issue - State: open - Opened by ekopylova almost 9 years ago

#19 - add homology search tools

Issue - State: closed - Opened by ekopylova almost 9 years ago - 1 comment

#18 - Update benchmark layout, add main launch script

Pull Request - State: closed - Opened by ekopylova almost 9 years ago - 1 comment

#17 - Issue 14

Pull Request - State: closed - Opened by ekopylova almost 9 years ago - 11 comments

#14 - script for swapping genes

Issue - State: closed - Opened by ekopylova about 9 years ago

#13 - launch_software.sh readlink & mkdir

Issue - State: open - Opened by ekopylova about 9 years ago

#12 - script for creating alf parameter file

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#11 - Pr/10

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#10 - initial commit for testing

Pull Request - State: closed - Opened by antgonza about 9 years ago

#9 - travis install of dependency software

Issue - State: open - Opened by ekopylova about 9 years ago

#8 - create env variables for PhyloNet & Jane 4 java jar files

Issue - State: open - Opened by ekopylova about 9 years ago

#7 - Example

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#6 - parse output function

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#5 - compute accuracy

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#4 - README updated, INSTALL & License added

Pull Request - State: closed - Opened by ekopylova about 9 years ago

#3 - distance method code optimizations

Issue - State: open - Opened by ekopylova about 9 years ago

#2 - ALF simulations, reformat input trees, launch benchmark scripts

Pull Request - State: closed - Opened by ekopylova about 9 years ago - 1 comment

#1 - The Distance Method HGT detection algorithm implemented in python

Pull Request - State: closed - Opened by ekopylova about 9 years ago - 3 comments