PhyloAcc pre-run stats
1. Run info (adaptive-test-branches)

The PhyloAcc interface was run on Sunday Oct 23, 2022 at 10:05:47 EDT on as follows:

/n/home07/gthomas/anaconda3/envs/phyloacc-pkg/bin/ -d /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/seq/ -m /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/mammal_acc1.mod -l /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/tree_coal_unit.mod -t turTru2;orcOrc1;odoRosDiv1;lepWed1;triMan1 -g monDom5;sarHar1;macEug2;ornAna1 -r adaptive -burnin 1000 -mcmc 7000 -n 24 -p 8 -j 20 -batch 25 -part holy-info,shared,holy-smokes -time 24 -o /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/adaptive-test-branches/ -phyloacc CONSERVE_PRIOR_B 0.1;ACCE_PRIOR_A 4; ACCE_PRIOR_B 0.5; CONSERVE_PROP 0.5; CONSERVE_RATE 0.3; TRIM_GAP_PERCENT 0.7 --overwrite
Alignment and batch info
Input alignments 2030
Alignments with 0 informative sites (removed) 1
Alignments for species tree model 28
Alignments for gene tree model 2001
Batches 83
Alignments per batch 25
Processes to use per batch 8
Batches using species tree model 2
Batches using gene tree model 81
Batches to submit to cluster simultaneously 20

See the full log file for more info.

Below are some summary plots. Raw data is also available in CSV format in the alignment stats file.

Run batches

The generated batches can be run with Snakemake with the following command:

snakemake -p -s /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/adaptive-test-branches/phyloacc-job-files/snakemake/run_phyloacc.smk --configfile /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/adaptive-test-branches/phyloacc-job-files/snakemake/phyloacc-config.yaml --profile /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/adaptive-test-branches/phyloacc-job-files/snakemake/profiles/slurm_profile --dryrun

Note that this includes the --dryrun option to check for possible errors before submitting jobs. If everything looks good after running that, feel free to remove the --dryrun option to submit the jobs to your cluster. You may also want to run this in the background using screen, tmux or some other terminal multiplexer to avoid disruptions due to server disconnects.

Coalescent tree provided for theta estimation

Since some or all of the loci will be processed with the gene tree model, a species tree with branch lengths in coalescent units was provided: /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/tree_coal_unit.mod

The branch lengths from this tree will be used in conjunction with the branch lengths in the input tree (which should be in units of relative number of substitutions) to estimate the theta parameter used in the gene tree model.

2. Input species tree
Species 62
Target species 5
Conserved species 53
Outgroup species 4
3. Distribution of locus lengths
Average alignment length 129.627
Median alignment length 92.0
Average sequence length (no gaps) per alignment 128.71
Median sequence length (no gaps) per alignment 90.742
4. Distribution of informative sites per locus
5. Correlation between variable and informative sites
6. sCF distributions per locus

Site concordance factors (sCF) summarize the number of sites in an alignment that support a branch in a given phylogeny.

Briefly, they are computed by sampling quartets of species around each branch in an unrooted tree and counting the number of decisive sites that match the topology of the sampled quartet in the phylogeny. See Minh et al. 2020 for more information.

Here, rather than averaging over branches for all alignments, we calculate sCF for each branch in each alignment separately.

7. sCF across all loci

Here, the species tree is shown with branches labeled by sCF across all branches (as described in Minh et al. 2020).

The tree in Newick format is located here.

The sCF stats per branch can be found in CSV format here.

8. Branch length vs. sCF for the species tree