naturalis/barcode-constrained-phylogeny issues and pull requests

#114 - Assess ITS potential

Issue - State: open - Opened by rvosa 4 months ago

#113 - Process plant barcodes

Issue - State: open - Opened by rvosa 4 months ago

#112 - Software sustainability improvements

Issue - State: open - Opened by rvosa 4 months ago

#111 - Odonata

Pull Request - State: closed - Opened by rvosa 5 months ago

#110 - CI/CD and testing

Issue - State: open - Opened by rvosa 5 months ago

#109 - Setup Lepidoptera

Issue - State: open - Opened by rvosa 5 months ago - 1 comment

#108 - Better file handling

Issue - State: open - Opened by rvosa 5 months ago

#107 - Provenance tracking, detecting errors

Issue - State: open - Opened by rvosa 5 months ago

#106 - Software publishing and visibility

Issue - State: open - Opened by rvosa 5 months ago

#105 - Attractive visualization

Issue - State: open - Opened by rvosa 5 months ago

#104 - Variable input species sets

Issue - State: open - Opened by rvosa 5 months ago

#103 - Periodic, automatically scheduled runs

Issue - State: open - Opened by rvosa 5 months ago

#102 - FAIR, versioned releases of result trees

Issue - State: open - Opened by rvosa 5 months ago

#101 - Scalability of large backbone grafting

Issue - State: open - Opened by rvosa 5 months ago

#100 - Scalability of large subsets

Issue - State: open - Opened by rvosa 5 months ago - 2 comments

#99 - Dynamic parallelization of rule execution

Issue - State: open - Opened by rvosa 5 months ago

#98 - Reproducibility of conda environments

Issue - State: open - Opened by rvosa 5 months ago

#97 - Check extreme outliers

Issue - State: open - Opened by rvosa 5 months ago

#96 - extinct taxa

Issue - State: closed - Opened by rvosa 6 months ago

#95 - family_fasta refinement needed

Issue - State: closed - Opened by rvosa 6 months ago - 1 comment

#94 - Update README.md

Pull Request - State: closed - Opened by rvosa 6 months ago - 1 comment

#93 - Non-flush alignments under certain conditions

Issue - State: open - Opened by rvosa 6 months ago - 1 comment

#92 - Update makeblastdb.sh

Pull Request - State: closed - Opened by rvosa 6 months ago - 1 comment

#91 - nucraw updates

Pull Request - State: closed - Opened by rvosa 6 months ago - 1 comment

#90 - results/fasta/family folder missing

Issue - State: closed - Opened by zahrag 6 months ago - 2 comments

#89 - DNA barcode sequence field in BOLD tsv

Issue - State: closed - Opened by zahrag 6 months ago - 4 comments

#88 - create_database.py nucraw to nuc

Issue - State: closed - Opened by AnnemiekeSchonthaler 6 months ago - 2 comments

#87 - Incongruencies in main README

Issue - State: closed - Opened by JWesseling 6 months ago - 2 comments

#86 - makeblastdb.sh shell script not portable

Issue - State: closed - Opened by JWesseling 6 months ago - 8 comments

#85 - Curate input data package

Issue - State: closed - Opened by rvosa 7 months ago - 2 comments

#84 - Create v1.1.0

Issue - State: closed - Opened by rvosa 7 months ago - 3 comments

#83 - create_database produces inconsistencies

Issue - State: closed - Opened by rvosa 7 months ago - 1 comment

#82 - Outgroup selection with blast

Issue - State: closed - Opened by rvosa 7 months ago - 3 comments

#81 - OpenToL 'broken' taxa

Issue - State: closed - Opened by rvosa 7 months ago - 1 comment

#80 - Add date/time stamp to log messages

Issue - State: closed - Opened by rvosa 7 months ago - 3 comments

#79 - Roadmap next release

Issue - State: open - Opened by rvosa 9 months ago

#78 - Submit to WorkflowHub

Issue - State: closed - Opened by rvosa 9 months ago - 1 comment

#77 - Picking exemplars

Issue - State: closed - Opened by rvosa 9 months ago - 3 comments

#76 - Reroot unrooted raxml subtree

Issue - State: closed - Opened by rvosa 9 months ago - 1 comment

#75 - RAxML placement and branch length optimization

Issue - State: closed - Opened by rvosa 9 months ago - 5 comments

#74 - Additional indexes needed

Issue - State: open - Opened by rvosa 9 months ago

#74 - Additional indexes needed

Issue - State: closed - Opened by rvosa 9 months ago

#73 - Data thinning

Issue - State: closed - Opened by rvosa 10 months ago

#72 - Incompatible dependency graphs across rules

Issue - State: closed - Opened by rvosa 10 months ago - 1 comment

#71 - Skip `temporary_database.db` step

Issue - State: closed - Opened by rvosa 10 months ago

#70 - Implementation status beyond raxml

Issue - State: closed - Opened by rvosa 10 months ago - 1 comment
Labels: to_do

#69 - Spurious pandas dependency errors

Issue - State: closed - Opened by rvosa 10 months ago
Labels: bug

#68 - Handling empty FASTA files

Issue - State: closed - Opened by rvosa 10 months ago
Labels: bug

#67 - hmmalign parameterization

Issue - State: closed - Opened by rvosa 11 months ago - 1 comment

#66 - Test master

Pull Request - State: closed - Opened by Naomivanes about 1 year ago

#65 - Fix hmm align issues

Pull Request - State: closed - Opened by Naomivanes about 1 year ago

#64 - Raxml

Pull Request - State: closed - Opened by NI-S about 1 year ago

#63 - Adding Hmmbuild

Pull Request - State: closed - Opened by NI-S about 1 year ago

#62 - raxml with parwise alignments

Issue - State: closed - Opened by Naomivanes about 1 year ago - 2 comments
Labels: question

#61 - fixed wrong input names and removed raxml-ng path

Pull Request - State: closed - Opened by Naomivanes about 1 year ago

#60 - Filter class

Pull Request - State: closed - Opened by Naomivanes about 1 year ago

#59 - remove redundant code

Pull Request - State: closed - Opened by Naomivanes about 1 year ago

#58 - additional values for alignment score + logging

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#57 - Hmm align

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#56 - MACSE to HMM

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: question

#55 - Hmmer align

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#54 - OPTION: Integrate perl tool db into custom db

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: enhancement

#53 - Use logging, not print statements

Issue - State: closed - Opened by rvosa over 1 year ago

#52 - Change alignment method

Issue - State: closed - Opened by Naomivanes over 1 year ago - 3 comments
Labels: to_do

#51 - Make families.txt's for both COI-5P familys and matK_rbcL

Issue - State: closed - Opened by Naomivanes over 1 year ago - 2 comments
Labels: to_do

#50 - Remove dashes (-) FASTA files

Issue - State: closed - Opened by Naomivanes over 1 year ago
Labels: to_do

#49 - Check barcode length

Issue - State: closed - Opened by Naomivanes over 1 year ago
Labels: to_do

#48 - Barcode database has no indexes or primary keys

Issue - State: closed - Opened by rvosa over 1 year ago - 4 comments
Labels: bug

#47 - Rule family_fasta

Issue - State: closed - Opened by rvosa over 1 year ago - 6 comments

#46 - add '# noqa: F821' to snakemake references in python scripts

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#45 - ERROR: Github when running a 'build-linux' job after pushing branch

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: bug

#44 - add rule all, raxlm directories, chose between NT and AA

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#43 - Add different Raxml command for AA alignments

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: to_do

#42 - Change raxml prefix

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment

#41 - FIX: No constraint tree needed for families with one ott

Issue - State: closed - Opened by Naomivanes over 1 year ago - 2 comments
Labels: bug

#40 - Release generated files using Zenodo

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: to_do

#39 - Documentation README /src

Issue - State: closed - Opened by Naomivanes over 1 year ago - 3 comments
Labels: documentation

#38 - Unit tests

Issue - State: closed - Opened by rvosa over 1 year ago - 1 comment

#37 - Directory changes

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#36 - The backbone logic

Issue - State: closed - Opened by rvosa over 1 year ago

#35 - macse in bin/

Issue - State: closed - Opened by rvosa over 1 year ago

#34 - Snake newick

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#33 - Documentation

Issue - State: closed - Opened by rvosa over 1 year ago - 1 comment
Labels: documentation

#32 - raxml and changing newick string

Pull Request - State: closed - Opened by NI-S over 1 year ago

#31 - Raxml tree

Pull Request - State: closed - Opened by NI-S over 1 year ago

#30 - Raxml tree

Pull Request - State: closed - Opened by NI-S over 1 year ago

#29 - Snakemake

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#28 - Open Tree of Life - extracting subtrees

Issue - State: closed - Opened by rvosa over 1 year ago - 1 comment
Labels: documentation

#27 - Correspondence between constraint tree and alignment

Issue - State: closed - Opened by rvosa over 1 year ago
Labels: documentation

#26 - Rewrite into snakemake pipeline

Issue - State: closed - Opened by Naomivanes over 1 year ago - 1 comment
Labels: to_do

#25 - save all constrain trees in a directory

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#24 - ERROR: Cannot find tree species

Issue - State: closed - Opened by Naomivanes over 1 year ago
Labels: bug

#23 - tree inference & data management

Issue - State: closed - Opened by rvosa over 1 year ago - 2 comments

#22 - change ids of alignment, automate creating trees

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#21 - remove exclamation mark

Pull Request - State: closed - Opened by NI-S over 1 year ago

#20 - Adding raxml

Pull Request - State: closed - Opened by NI-S over 1 year ago

#19 - added docstring documentation

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#18 - removed param from function

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#17 - Opentol mapping

Pull Request - State: closed - Opened by Naomivanes over 1 year ago

#16 - Merge pull request #15 from naturalis/main

Pull Request - State: closed - Opened by NI-S over 1 year ago

GitHub / naturalis/barcode-constrained-phylogeny issues and pull requests