Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / brettc/partitionfinder issues and pull requests

#140 - Add python3 and package manager

Pull Request - State: closed - Opened by Doubravka about 1 month ago - 1 comment

#137 - TIM model

Issue - State: closed - Opened by zcalamari about 4 years ago - 1 comment

#136 - Running ~20 loci dataset

Issue - State: open - Opened by aberaslop over 4 years ago - 1 comment

#135 - Error about working directory via

Issue - State: open - Opened by zhounan1356 almost 5 years ago - 1 comment

#134 - Error 522 to download anaconda

Issue - State: open - Opened by glichtenstein about 5 years ago - 1 comment

#133 - Link to the example dataset in the tutorial is broken

Issue - State: open - Opened by joelnitta over 5 years ago

#131 - user_tree_topology handling

Issue - State: open - Opened by carloliveros almost 6 years ago

#130 - --rcluster-max default

Issue - State: closed - Opened by carloliveros almost 6 years ago - 1 comment

#129 - partitionfinder error on WIN7 32 bit

Issue - State: closed - Opened by dongzhang0725 almost 6 years ago - 2 comments

#128 - Manual in Chinese

Issue - State: open - Opened by roblanf over 6 years ago

#127 - HDF5 error

Issue - State: open - Opened by roblanf about 7 years ago - 1 comment

#126 - Buffer2

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

#125 - Fix: call scipy.misc.comb with exact=True

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

#124 - buffer size issue

Issue - State: open - Opened by roblanf over 7 years ago - 10 comments

#123 - remove DUMMY and DUMMY2 models

Issue - State: closed - Opened by roblanf almost 8 years ago - 1 comment

#122 - Move shell scripts into Makefile

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

#121 - Add license to root.

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

#120 - Manual in md

Pull Request - State: open - Opened by alephreish about 8 years ago - 13 comments

#119 - chunk tasks for analysis

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

#118 - some very minor changes

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

#117 - added a lightweight dependency checker

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

#116 - Feature/clean tiger

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

#115 - Feature/ml default tree

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

#114 - Feature/kmeans manyparts

Pull Request - State: open - Opened by roblanf over 8 years ago - 1 comment
Labels: in progress

#113 - Manual in md?

Issue - State: closed - Opened by alephreish over 8 years ago - 6 comments

#112 - Script execution

Issue - State: closed - Opened by alephreish over 8 years ago - 5 comments

#111 - Input and output

Issue - State: closed - Opened by alephreish over 8 years ago - 3 comments

#110 - fix deprecated numpy issue

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

#109 - LG4X is a pain

Issue - State: closed - Opened by roblanf over 8 years ago - 3 comments

#108 - Feature/morph tiger rates

Pull Request - State: closed - Opened by pbfrandsen over 8 years ago

#107 - Fix RAxML warning message about GTR+G and GTR+I+G

Issue - State: closed - Opened by pbfrandsen over 8 years ago - 2 comments

#106 - Discuss: make an ML starting tree the default

Issue - State: closed - Opened by roblanf over 8 years ago - 7 comments

#105 - Feature/morph

Pull Request - State: closed - Opened by wrightaprilm over 8 years ago

#104 - Feature/morph

Pull Request - State: closed - Opened by roblanf over 8 years ago

#103 - Discuss: TIGER implementations are confusing

Issue - State: closed - Opened by roblanf over 8 years ago - 9 comments

#102 - Feature/morph

Pull Request - State: closed - Opened by wrightaprilm over 8 years ago

#101 - add morphology to the manual

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

#100 - add references for PF morphology methods

Issue - State: closed - Opened by roblanf over 8 years ago - 2 comments

#99 - new krmeans algorithm

Pull Request - State: closed - Opened by roblanf over 8 years ago

#98 - failing tests

Issue - State: closed - Opened by roblanf over 8 years ago - 12 comments

#97 - add tests for morphology

Issue - State: closed - Opened by roblanf over 8 years ago - 22 comments

#96 - check morphology models

Issue - State: closed - Opened by roblanf over 8 years ago - 4 comments

#95 - implement krmeans

Pull Request - State: closed - Opened by roblanf over 8 years ago

#94 - commas removed between sites in MrBayes block

Pull Request - State: closed - Opened by marekborowiec over 8 years ago - 1 comment

#93 - min subset size

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

#92 - MrBayes block

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

#91 - Prevent partitionfinder crash when passing in a single partition.

Pull Request - State: closed - Opened by biologyguy over 8 years ago - 5 comments

#90 - Catch edge case of single partition in greedy algorithm

Pull Request - State: closed - Opened by biologyguy over 8 years ago - 2 comments

#89 - finding anaconda python

Issue - State: closed - Opened by roblanf almost 9 years ago - 7 comments

#88 - 2.0.0-pre11 manual mentions non-existant command line flags

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

#87 - Package for Debian

Issue - State: closed - Opened by kdm9 almost 9 years ago - 2 comments

#86 - user scheme reporting

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

#84 - Feature/ml tree

Pull Request - State: closed - Opened by roblanf almost 9 years ago

#83 - compile two versions of RAxML

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

#82 - Develop

Pull Request - State: closed - Opened by roblanf almost 9 years ago

#81 - error in mr bayes block

Issue - State: closed - Opened by roblanf about 9 years ago - 1 comment

#80 - Feature/fastercluster

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

#79 - include category for lie markov models in models.cv

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

#78 - Feature/merge little subsets

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

#77 - Feature/mrbayes output

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

#76 - feature request for csv summary of all schemes

Issue - State: closed - Opened by roblanf about 9 years ago - 1 comment

#75 - update manual with clear instructions on anaconda / python version

Issue - State: closed - Opened by roblanf about 9 years ago - 1 comment

#74 - Error 2 in alignment parsing

Issue - State: closed - Opened by roblanf about 9 years ago - 3 comments

#73 - Error in alignment parsing

Issue - State: closed - Opened by roblanf about 9 years ago - 2 comments

#72 - check_state_probs needs some tests

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

#71 - Enable valid character checking in the alignment parser?

Issue - State: closed - Opened by brettc about 9 years ago - 2 comments

#70 - Feature/complete alignments

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

#69 - Add Phyml parsing tests

Issue - State: closed - Opened by brettc about 9 years ago - 1 comment

#68 - Feature/greedy speedy

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

#67 - Outstanding TODO list items (from removed TODO.txt)

Issue - State: closed - Opened by brettc over 9 years ago - 2 comments

#66 - Feature/1kite bugfix2

Pull Request - State: closed - Opened by roblanf over 9 years ago

#65 - loading big alignments

Issue - State: closed - Opened by roblanf over 9 years ago - 4 comments

#64 - Update minimum versions for python (and anaconda?) in Manual

Issue - State: closed - Opened by brettc over 9 years ago - 1 comment

#63 - Feature/1kitebugfix1

Pull Request - State: closed - Opened by roblanf over 9 years ago

#62 - bug in rcluster

Issue - State: closed - Opened by roblanf over 9 years ago - 1 comment

#61 - bug in fabricating subsets

Issue - State: closed - Opened by roblanf over 9 years ago - 7 comments

#60 - parsing RAxML output

Issue - State: closed - Opened by roblanf over 9 years ago - 5 comments

#59 - PF 2.0 dies with an error when trying to join threads

Issue - State: closed - Opened by pbfrandsen over 9 years ago - 3 comments

#58 - add --no-bfgs to all RAxML commandlines

Issue - State: closed - Opened by roblanf over 9 years ago - 3 comments

#57 - fix tiger_DNA import in kmeans

Issue - State: closed - Opened by roblanf over 9 years ago - 3 comments

#56 - Manually check lastest phyml

Issue - State: closed - Opened by brettc over 9 years ago - 3 comments

#55 - bump the version number to 2.0.0

Issue - State: closed - Opened by roblanf over 9 years ago - 3 comments

#54 - add section to manual on major differences with PF1

Issue - State: closed - Opened by roblanf over 9 years ago - 13 comments

#53 - update RAxML to very latest version

Issue - State: closed - Opened by roblanf over 9 years ago - 14 comments

#52 - fix rerun tests

Issue - State: closed - Opened by roblanf over 9 years ago - 1 comment

#51 - fix full tests with results comparisons

Issue - State: closed - Opened by roblanf over 9 years ago - 1 comment

#50 - fix parser tests

Issue - State: closed - Opened by roblanf over 9 years ago - 2 comments

#49 - tigger matrix

Issue - State: closed - Opened by roblanf over 9 years ago - 2 comments

#48 - Installations on windows network drives seem to fail

Issue - State: open - Opened by brettc over 9 years ago

#47 - PhyML output filename conventions on linux

Issue - State: closed - Opened by kgori over 9 years ago - 2 comments

#46 - New model names break tests

Issue - State: closed - Opened by brettc over 9 years ago - 2 comments

#45 - checks on bad subsets are not working

Issue - State: closed - Opened by roblanf over 9 years ago - 1 comment

#43 - cython tiger implementation has a flag requiring OS 10.8 or higher

Issue - State: closed - Opened by pbfrandsen over 9 years ago - 3 comments

#42 - user schemes seem to be broken

Issue - State: closed - Opened by roblanf over 9 years ago - 2 comments

#41 - Add a Gitter chat badge to README.md

Pull Request - State: open - Opened by gitter-badger over 9 years ago