phlag-mammalian-analysis

Phlag analysis of the mammalian phylogeny This repository contains the Phlag analysis results, gene trees, species trees, and supporting data for the mammalian dataset (experiment E4) presented in: Şapcı AOB, Arasti S, Braun EL, Mirarab S. Phlag: Scalable detection of genomic regions with unexplained phylogenetic heterogeneity. Bioinformatics, ISMB issue (2026). Phlag is available at github.com/bo1929/phlag. Files alltrees.tree.gz: Compressed gene trees (19,465 trees) inferred from chromosome 3 of the mammalian alignment by Foley et al.. We estimated gene trees using IQ-TREE under the GTR+G4 model from 1Kbp subalignments selected with minimum missing data from each 10Kbp segment. labelled_species_tree.nwk: Species tree in Newick format with 241 mammalian taxa and internal nodes labelled I0–I239 with branch lengths. ref.topology: Reference species tree topology. qqs.txt: Precomputed quartet quartet site (QQS) frequencies for all gene trees and internal branches, used as input to Phlag. pos: Genomic positions (on the human chromosome 3 coordinate) for each gene tree window. order.txt: File identifiers for each gene tree locus/window. taxon_map.txt: Mapping from internal node labels (I0–I239) to taxonomic family names via NCBI taxonomy. taxon_map_order.txt: Mapping from internal node labels to taxonomic order names. taxdump.tar.gz: NCBI taxonomy database dump used by map_lca.py. map_lca.py: Python script (using ete3) for resolving internal node labels to their lowest common ancestor in NCBI taxonomy. prep.sh: Preprocessing script that extracts Hellinger distances from Phlag prediction files and produces summary files. echo_cmd.sh: Script containing the Phlag commands used to generate predictions under different hyperparameter settings. Phlag predictions all_pred-{PARAMS}-chr3/: Directories containing Phlag output for chromosome 3 under different hyperparameter combinations. Each directory contains: distances_chr3.txt: Hellinger distance between the null and alternative emission distributions for each internal branch. pred-I{NODE}-{PARAMS}.txt: Per-branch prediction file containing the Phlag command, the modified species tree, decoded state predictions, and the distance metric. The naming convention encodes hyperparameters as follows: eap{beta}: expected number of anomalies (--expected-num-anomalies), e.g., eap50: beta = 50. ep{1-rho}: expected anomaly proportion (--expected-anomaly-proportion), e.g., ep005: 1-rho = 0.05. penalty{lambda} / npenalty{N}: prior penalty strength (lambda), with n prefix indicating a negative value. Available parameter combinations: all_pred-eap50_ep005_penalty15-chr3 all_pred-eap50_ep002_penalty15-chr3 all_pred-eap40_ep005_penalty15-chr3 all_pred-eap100_ep005_penalty15-chr3 (the main paper analysis) all_pred-eap100_ep010_penalty15-chr3 Description Phlag was applied to 19,465 gene trees inferred from chromosome 3 of the mammalian genome alignment by Foley et al., covering 241 species. Gene trees were estimated by selecting 1Kbp subalignments with minimum missing data from each 10Kbp segment and running IQ-TREE under GTR+G4. Phlag was applied to 136 internal branches under key mammalian orders (Carnivora, Chiroptera, Primates, Artiodactyla, and Rodentia), retaining branches that define a quadripartition in at least 90% of the gene trees. Each branch was analyzed individually (single focal branch) using the prior-updated mode with topology-order emissions.