Issues

Per-Site Sankoff Validation Plan
matsengrp/larch#108 · opened on Feb 2, 2026
Design: Site-Specific Weighted Parsimony (Sankoff Algorithm)
matsengrp/larch#106 · opened on Dec 4, 2025
1
UA Free parsimony
matsengrp/larch#100 · opened on Sep 9, 2025
documentation
matsengrp/larch#98 · opened on Aug 12, 2025
Comparing the MP landscape with SPRTA's support scores
matsengrp/larch#97 · opened on Aug 3, 2025
Optimized DAG contains nodes with identical LeafSets and CGs but different node IDs.
matsengrp/larch#86 · opened on Aug 6, 2024
Add LeafSets directly to the fragment
matsengrp/larch#73 · opened on Jan 9, 2024
Beast tree loading
matsengrp/larch#65 · opened on Sep 12, 2023
1
collapsing the DAG
matsengrp/larch#49 · opened on Apr 10, 2023
2
Benchmarking on very large DAGs
matsengrp/larch#40 · opened on Nov 16, 2022
Subsetting (trimming/sampling) the history DAG efficiently
matsengrp/larch#39 · opened on Nov 16, 2022
Summary of goals
matsengrp/larch#36 · opened on Nov 10, 2022
Counting the number of trees in which each node (or clade) takes part
matsengrp/larch#30 · opened on Oct 17, 2022
Sampling from the DAG's topological fringe
matsengrp/larch#29 · opened on Oct 17, 2022
Sampling from the DAG with probabilities (and constraints)
matsengrp/larch#28 · opened on Oct 12, 2022
2
Indexing Histories
matsengrp/larch#27 · opened on Oct 12, 2022
1
Change reference sequence of MAD
matsengrp/larch#17 · opened on Jul 28, 2022
Add install target
matsengrp/larch#12 · opened on Jul 5, 2022
collapse nodes
matsengrp/larch#2 · opened on Apr 27, 2022