FunVIP 0.5.7

What's Changed

Added --cluster_max_target_seqs option. Increasing this may help finding better outgroup,
while search step would be slower and result larger intermediate file size

• 0.5.7 by @Changwanseo in #67
  Full Changelog: 0.5.6...0.5.7

FunVIP 0.5.6

• Small optimizations in tree_interpretation
• Better deterministic behavior by fixing random seed

What's Changed

• 0.5.5 installation md by @Changwanseo in #65
• FunVIP 0.5.6 by @Changwanseo in #66

Full Changelog: 0.5.5...0.5.6

FunVIP 0.5.5

What's Changed

• Native support for Apple Silicon has launched!

• 0.5.5 by @Changwanseo in #64
  Full Changelog: 0.5.4...0.5.5

FunVIP 0.5.4

What's Changed

• Merge descriptions from main by @Changwanseo in #62
• FunVIP 0.5.4 by @Changwanseo in #63

Full Changelog: 0.5.3...0.5.4

FunVIP 0.5.3

• Reordered manage_unicode calls to run before string manipulations for genus, species, and group fields to handle terminal spaces correctly.
• Improved sequence handling to prevent unicode errors
• Updated the project version to 0.5.3 in pyproject.toml.

FunVIP 0.5.2

What's Changed

• FunVIP 0.5.1 release pull request by @Changwanseo in #58
  Full Changelog: 0.5.0...0.5.2

• Fixed FunVIP cannot read csv files with newline characters within quoted string
• Fixed non-overlapping sequence detection indicating wrong pair of sequences
• Fixed non-overlapping sequence detection indicating wrong pair of sequences

FunVIP 0.5.1

Release Notes

• Fixed "&" sign in svg fails visualization

FunVIP 0.5.0

Update Notice: FunVIP 0.5.0 Released

You can update to the latest versions using:

pip install FunVIP --upgrade

Release Notes

• Fixed issue with suspicious group detection - use the new --nosuspicious flag if you prefer the previous behavior
• Added --terminate option - pipeline will stop when problematic alignments are detected
• Enhanced diagnostics for alignments without overlapping regions - now identifies which sequence pairs are causing issues and provides a summary at the end
• Fixed IQ-TREE crashes under specific conditions
• Fixed modeltest-ng compatibility with Windows
• Added bootstrap values to original tree SVG files
• Corrected column names in Penicillium test dataset
• Improved rerooting algorithm
• Added temporary fix for crashes when using more than 100 threads
• Updated GenMine dependency to version 1.3.0
• Increased default font size for better readability
• Changed default alignment to right-justify sequence IDs

FunVIP 0.4.1

• Enabled modeltest-ng dependency for Windows system
• Fixed iqtree terminating with certain modeltest condition

FunVIP 0.4.0

This is official release of FunVIP version, in published article.
Few bug fixes and improvments were included.

Patch notes from 0.3.25

• Added option subgenus for --level
• GenMine sequence download will be performed in randomized order to avoid NCBI ban if FunVIP is too frequently performed
• Fixed zero length sequences terminating model selection