CHANGELOG.md

v0.8 [02.02.2026]

Changes

• Add a first version of Sima de los huesos and Denisovan diagnostic positions to the tree XML
• Add a upper hierarchie (NA'SIMA'DEN) for the common postions of Neanderthal, Sima and Denisova
• Add a first version of a final report
• Add stats and output-files for Deduped and Deaminated sequences separately
• Remove the min_support and max_gaps flags, as they are not helpful in mixed samples (that was the original intention...)

v0.7 [30.01.2026]

Changes

• add Neanderthal haplogroups to the phylotree XML file, as published in Andreeva et al. 2022
• Update LICENSE to include the MIT LICENSE of the Institute of Genetic Epidemiology, Insbruck
• Include the --penalty_plus flag (default: 2) to display nodes with higher penalty than the lowest.

v0.6 [19.01.2026]

Changes

• add TotalMismatch column, indicating the total number of mismatches in the branch support between covered and supported positions
• add SumOfGaps column, that shows the accumulated number of gaps in this branch
• add DistanceToBest column that shows the difference of supported branch positions to the maximum number of supported positions in any branch
• update the Penalty column to show SumOfGaps + TotalMismatch + DistanceToBest
• Rename (and add) output tree-tables
  • rename the full table from all_groups to raw
  • add a table that shows the path to the nodes with the best two (minimum) penalty scores (best)

v0.5 [14.01.2026]

Changes

• Add the RequiredGaps column in the summary that, looking back, counts how many intermediate nodes were skipped to get there (different to the Penalty column that looks forward to the closest child)
• introduce the --max_gaps and --min_support flags to filter the tree based on the BranchSupport and the RequiredGaps columns

v0.4 [12.01.2026]

Changes

• Reformat parse_pylotree code (more readable and maintainable)
• Use BranchSupport as a new filter-metric
• Update the output-files (All Nodes, 70% Support, 70% Support + Max 3 Gaps)
• Add MIT LICENSE

v0.3

Changes

• Call a position with ! (re-mutation) only as 'found', if the same position was not requested before. This is necessary, because they hit tip-positions way too often and accumulate hits in large branches.
  • e.g. 16311T in L3 -> 16311T! in U1b3 (not found)
  • e.g. 16311T in L3 -> 16311A! in U5? (found)
• Second output (groups with coverage) now clips all nodes that have a penalty >= 3
  • this can make the second file less useful in some instances, but much more useful in many more :)