HGT-Start

HGTstart takes a fasta format file containing all protein sequences used to predict HGTs as input.

Notified by email

Job Title

Input required

Protein file(FASTA format)

Content after the first space in ID will be ignored

Annotation file (gff, gff3 or gtf format, guess from file extention)

HGTstart require strictly GFF files of REFSEQ format. Convert your format if it doesn't match before running it.

Genome file (FASTA format)

NCBI taxnomy id of query species

taxid

Usage sample.faa sample.gff3 sample.fna

Optional parameters

Optional parameters of step 0 to 2

Tool used to search homologous

diamond

blastp

Tool used to build tree

FastTree

iqtree

Optional parameters of step 0, 1, 2

--total <num>

total number of seqs inclued in tree (default=60)

--phylum <num>

maximal number of seqs in each phylum (default=10)

--class <num>

maximal number of seqs in each class (default=10)

--self <num>

maximal number of seqs in each selfspecies (default=10)

--length <str>

minimal sequence length to start with (default=40)

Optional parameters of step 3

--donor <str>

Donor(s); separate multiple donors with comma

--cutoff <num>

node support Cutoff (default=0)

--optional <str>

Optional taxa allowed in monophyletic ingroup

--ignore <str>

taxa to be Ignored while screening trees

--ssnode <num>

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

--asnode <num>

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

--minimalReceptorNumber <num>

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

--minimalDonorNumber <num>

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

--outgroupsize <num>

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

Optional parameters of step 4

--minimalAI <num>

minimal value of Alien Index to filter a HGT events (default=0)

--minmalBrchLnth <num>

minimal value of Index of Branch Length to filter a HGT events (default=2)

--minmalHU <num>

minimal value of BLAST Score Index to filter a HGT events (default=0)

Optional parameters of step 5

levels to deteimine the exogenous from blast hit

phylum

kingdom

superkingdom

JOB UUID:

Predict HGTs

HGTstart takes a fasta format file containing all protein sequences used to predict HGTs as input.

Notified by email

Input required

Optional parameters

Optional parameters of step 0 to 2

Modal title