HGT-Start

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Predict HGTs

Predict HGTs

HGTStart v5 takes a FASTA file containing exactly one protein sequence (plus its genome FASTA, annotation file and NCBI taxonomy id) to predict HGTs.

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Job Title

Input required

Protein file (FASTA format)

One TARGET protein per job — put it as the FIRST record. You may include its neighboring proteins from the same genome as additional records for flanking-gene context. Content after the first space in ID will be ignored.

Example: XP_015873120.1 (histone-like HGT gene of Ziziphus jujuba) + chromosome proteins

Annotation file (gff, gff3 or gtf format, guessed from file extension)

Provide the annotation of your genome. GFF3 / GTF / GFF are accepted; please make sure protein IDs in the annotation match the FASTA header.

Example: chromosome NC_029680.1 annotation (14 MB)

Genome file (FASTA format)

Example: chromosome NC_029680.1 sequence (28 MB)

NCBI taxnomy id of query species

taxid

Example: 326968 (Ziziphus jujuba)

Usage sample.faa sample.gff sample.fna

Optional parameters

Search & trees (steps 1-2)

Tool used to search homologous

diamond

DIAMOND search engine (fixed)

Tool used to build tree

FastTree

iqtree

Homolog search & tree building

Homolog sampling and search parameters are managed automatically by the pipeline (DIAMOND search, IQ-TREE / FastTree tree building).

HGT inference (step 3)

-don <str>

Donor(s); separate multiple donors with comma

-cut <num>

node support Cutoff, 0-100 (70 recommended; 0 = skip)

-opt <str>

Optional taxa allowed in monophyletic ingroup

-ign <str>

taxa to be Ignored while screening trees

-ssn <num>

minimal Strongly Supported Nodes uniting query and donors(default=1)

-asn <num>

minimal number of All Supporting Nodes uniting query and donors(default=2)

-mrn <num>

minimal number of Receptors in a nested position (default =2)

-mdn <num>

minimal number of Donors in a nested position (default =2)

-ogs <num>

minimal OutGroup Size for a tree to be considered valid(default=5)

HGT inference filters

-minAI <num>

minimal value of Alien Index to filter HGT events (small value = keep more candidates)

-minHBL <num>

minimal value of Branch Length Index to filter HGT events (small value = keep more candidates)

-minHU <num>

minimal value of BLAST Score Index to filter HGT events (small value = keep more candidates)

Taxon resolution & genomic context

levels to deteimine the exogenous from blast hit

phylum

kingdom

superkingdom

-flank-n <num>

coding loci per side of an HGT block (default=1)

-timeHGT (molecular dating)

enable treePL dating (slower, adds divergence times)

JOB UUID: