EvanForsythe ERCnet issues

EvanForsythe / ERCnet

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added plain text network output and new network tracking files

#147 EvanForsythe closed 2 weeks ago
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Update README.md

#146 EvanForsythe closed 1 month ago
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Iqtree

#145 EvanForsythe closed 1 month ago
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refactored ERC_analyses.py to achieve a 10-fold speed increase

#144 EvanForsythe closed 1 month ago
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Update README.md

#143 EvanForsythe closed 1 month ago
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Pairwise

#142 EvanForsythe closed 1 month ago
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added several scripts and functions to track performance

#141 EvanForsythe closed 1 month ago
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Update README.md

#140 EvanForsythe closed 1 month ago
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Update README.md

#139 EvanForsythe closed 1 month ago
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Run tracking

#138 EvanForsythe closed 1 month ago
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added new lengths

#137 EvanForsythe closed 1 month ago
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Update README.md

#136 EvanForsythe closed 2 months ago
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added a script for simulating coevolving proteomes

#135 EvanForsythe closed 2 months ago
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Add run data logs

#134 EvanForsythe opened 2 months ago
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Update README.md

#133 EvanForsythe closed 3 months ago
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Update README.md

#132 EvanForsythe closed 3 months ago
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changed binary trees and correlation analyses

#131 EvanForsythe closed 3 months ago
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Update README.md

#130 EvanForsythe closed 4 months ago
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Update README.md

#129 EvanForsythe closed 4 months ago
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Update README.md

#128 EvanForsythe closed 4 months ago
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Update README.md

#127 EvanForsythe closed 4 months ago
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TSV instead of CSV

#126 EvanForsythe opened 4 months ago
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Update README.md

#125 EvanForsythe closed 4 months ago
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altered dataframe column renaming so that the first column isn't lost

#124 EvanForsythe closed 5 months ago
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Add overlapping branches filter to ERC_analyses.py or Network_analyses.py?

#123 EvanForsythe opened 5 months ago
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Add non-bifurcating check to Get_subtree.R

#122 EvanForsythe opened 5 months ago
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Hide Parallel() output from phylogenomics.py output

#121 EvanForsythe opened 5 months ago
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Add Non-binary_subtrees.txt to the diagram

#120 EvanForsythe opened 5 months ago
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ERCnet doesn't write network as a plain text file

#119 EvanForsythe opened 6 months ago
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Add check to make sure folders aren't empty before proceeding to next step

#118 EvanForsythe opened 6 months ago
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Need to add --scrict argument to the readme documentation for the Network analyses.

#117 EvanForsythe opened 6 months ago
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added a check for empty files

#116 EvanForsythe closed 7 months ago
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Blank alignments output by mafft

#115 EvanForsythe opened 7 months ago
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Unexpected behavior when RAXML executable can't be found

#114 linxlane opened 8 months ago
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fixed the dataframe drop issue

#113 EvanForsythe closed 8 months ago
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Add python 3 yml file

#112 linxlane closed 8 months ago
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fixed taper error when called from python

#111 EvanForsythe closed 8 months ago
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added a check for seqIDs that are too long or identical/duplicate

#110 EvanForsythe closed 9 months ago
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Numpy Version Conflict

#109 AshleyNDoerfler opened 9 months ago
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Explore_filters table formatting issues

#108 EvanForsythe opened 11 months ago
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Update README.md

#107 tgattsIV closed 1 year ago
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Idea for a feature that allows users to add their own gene trees to Phylogenomics.py

#106 EvanForsythe opened 1 year ago
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Tony parallel erc fix

#105 tgattsIV closed 1 year ago
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Fixes several small issues.

#104 tgattsIV closed 1 year ago
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Solves RAxML core issue and sets default core_distribution to 4

#103 tgattsIV closed 1 year ago
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Both the ERC_analysis and Network_analysis Readme sections are out of date

#102 tgattsIV opened 1 year ago
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Adds benchmarking feature to GTST_reconciliation.py and Network_analysis.py

#101 tgattsIV closed 1 year ago
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Adds FDR feature to Network Analysis

#100 tgattsIV closed 1 year ago
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added a feature that writes a .graphml file compatible with Cytoscape

#99 EvanForsythe closed 1 year ago
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Add instructions for how to 'rerun' orthofinder if the species tree isn't correct

#98 EvanForsythe opened 1 year ago
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