diverse_seq provides alignment-free algorithms to facilitate phylogenetic workflows
diverse-seq implements computationally efficient alignment-free algorithms that enable efficient prototyping for phylogenetic workflows. It can accelerate parameter selection searches for sequence alignment and phylogeny estimation by identifying a subset of sequences that are representative of the diversity in a collection. We show that selecting representative sequences with an entropy measure of k-mer frequencies correspond well to sampling via conventional genetic distances. The computational performance is linear with respect to the number of sequences and can be run in parallel. Applied to a collection of 10.5k whole microbial genomes on a laptop took ~8 minutes to prepare the data and 4 minutes to select 100 representatives. diverse-seq can further boost the performance of phylogenetic estimation by providing a seed phylogeny that can be further refined by a more sophisticated algorithm. For ~1k whole microbial genomes on a laptop, it takes ~1.8 minutes to estimate a bifurcating tree from mash distances.
You can read more about the methods implemented in diverse_seq in the preprint here.
dvs prep: preparing the sequence data
Convert sequence data into a more efficient format for the diversity assessment. This must be done before running either the nmost or max commands.
CLI options for dvs prep
``` Usage: dvs prep [OPTIONS] Writes processed sequences to advs nmost: select the n-most diverse sequences
Selects the n sequences that maximise the total JSD. We recommend using nmost for large datasets.
Note A fuller explanation is coming soon!
Options for command line dvs nmost
``` Usage: dvs nmost [OPTIONS] Identify n seqs that maximise average delta JSD Options: -s, --seqfile PATH path to .dvseqs file [required] -o, --outpath PATH the input string will be cast to Path instance -n, --number INTEGER number of seqs in divergent set [required] -k INTEGER k-mer size [default: 6] -i, --include TEXT seqnames to include in divergent set -np, --numprocs INTEGER number of processes [default: 1] -L, --limit INTEGER number of sequences to process -v, --verbose is an integer indicating number of cl occurrences [default: 0] -hp, --hide_progress hide progress bars --help Show this message and exit. ```Options for cogent3 app dvs_nmost
The `dvs nmost` is also available as the [cogent3 app](https://cogent3.org/doc/app/index.html) `dvs_nmost`. The result of using `cogent3.app_help("dvs_nmost")` is shown below. ``` Overview -------- select the n-most diverse seqs from a sequence collection Options for making the app -------------------------- dvs_nmost_app = get_app( 'dvs_nmost', n=10, moltype='dna', include=None, k=6, seed=None, ) Parameters ---------- n the number of divergent sequences moltype molecular type of the sequences k k-mer size include sequence names to include in the final result seed random number seed Notes ----- If called with an alignment, the ungapped sequences are used. The order of the sequences is randomised. If include is not None, the named sequences are added to the final result. Input type ---------- ArrayAlignment, SequenceCollection, Alignment Output type ----------- ArrayAlignment, SequenceCollection, Alignment ```dvs max: maximise variance in the selected sequences
The result of the max command is typically a set that are modestly more diverse than that from nmost.
Note A fuller explanation is coming soon!
Options for command line dvs max
``` Usage: dvs max [OPTIONS] Identify the seqs that maximise average delta JSD Options: -s, --seqfile PATH path to .dvseqs file [required] -o, --outpath PATH the input string will be cast to Path instance -z, --min_size INTEGER minimum size of divergent set [default: 7] -zp, --max_size INTEGER maximum size of divergent set -k INTEGER k-mer size [default: 6] -st, --stat [stdev|cov] statistic to maximise [default: stdev] -i, --include TEXT seqnames to include in divergent set -np, --numprocs INTEGER number of processes [default: 1] -L, --limit INTEGER number of sequences to process -T, --test_run reduce number of paths and size of query seqs -v, --verbose is an integer indicating number of cl occurrences [default: 0] -hp, --hide_progress hide progress bars --help Show this message and exit. ```Options for cogent3 app dvs_max
The `dvs max` is also available as the [cogent3 app](https://cogent3.org/doc/app/index.html) `dvs_max`. ``` Overview -------- select the maximally divergent seqs from a sequence collection Options for making the app -------------------------- dvs_max_app = get_app( 'dvs_max', min_size=5, max_size=30, stat='stdev', moltype='dna', include=None, k=6, seed=None, ) Parameters ---------- min_size minimum size of the divergent set max_size the maximum size of the divergent set stat either stdev or cov, which represent the statistics std(delta_jsd) and cov(delta_jsd) respectively moltype molecular type of the sequences include sequence names to include in the final result k k-mer size seed random number seed Notes ----- If called with an alignment, the ungapped sequences are used. The order of the sequences is randomised. If include is not None, the named sequences are added to the final result. Input type ---------- ArrayAlignment, SequenceCollection, Alignment Output type ----------- ArrayAlignment, SequenceCollection, Alignment ```dvs ctree: build a phylogeny using k-mers
The result of the ctree command is a newick formatted tree string without distances.
Note A fuller explanation is coming soon!