Pipeline flow examples

Run blast

Blast subroutine selection selects protein files for blastp protein.fasta

Blast subroutine selection selects protein files for blastn nuclein.fasta

Run diamond

Blast subroutine selection selects protein files for blastp protein.fasta

Blast subroutine selection selects protein files for blastx nuclein.fasta

Fabaceae blast and match

Blast subroutine selection selects protein files for blastp protein.fasta

Blast subroutine selection selects protein files for blastn nuclein.fasta

Blast dotplot

Upload the blast result fileBlastp.txt

Upload the chromosome lens file for Species 1Species 1 lens.txt

Upload the chromosome lens file for Species 2Species 2 lens.txt

Upload the gff file of Species 1Species 1 gff.gff

Upload the gff file of Species 2Species 2 gff.gff

MCScanX

Upload the blast result fileBlastp.txt

Upload the gff file of SpeciesSpecies 2 gff.gff

Colinearscan

Upload the blast result fileZM-OS.filter.blast

Upload the gff file of SpeciesSpecies OS.gff

Upload the gff file of SpeciesSpecies ZM.gff

WGDI Syntenic

Upload the blast result filePvu_Mtr.blast

Upload the chromosome lens file for Species 1 Species Pvu.lens

Upload the chromosome lens file for Species 2 Species Mtr.lens

Upload the gff file of Species 1 Species Pvu.gff

Upload the gff file of Species 2 Species Mtr.gff

Block dotplot

Upload the blast result filePvu_Mtr.blast

Upload the blast result filePvu_Mtr.block

Upload the chromosome lens file for Species 1 Species Pvu.lens

Upload the chromosome lens file for Species 2 Species Mtr.lens

Upload the gff file of Species 1 Species Pvu.gff

Upload the gff file of Species 2 Species Mtr.gff

KaKs calculate

Upload the CDS result fileCDS file

Upload the blast result fileBlock file

Ks dotplot

Upload the blast result filePvu_Mtr.blast

Upload the blast result filePvu_Mtr.block

Upload the blast result filePvu_Mtr.ks

Upload the chromosome lens file for Species 1 Species Pvu.lens

Upload the chromosome lens file for Species 2 Species Mtr.lens

Upload the gff file of Species 1 Species Pvu.gff

Upload the gff file of Species 2 Species Mtr.gff

WGDI-kaks

Upload the blast result file Pep file

Upload the CDS result file CDS file

Upload the blast result file Block file

WGDI blockinfo

Upload the blast result filePvu_Mtr.blast

Upload the blast result filePvu_Mtr.block

Upload the blast result filePvu_Mtr.ks

Upload the chromosome lens file for Species 1 Species Pvu.lens

Upload the chromosome lens file for Species 2 Species Mtr.lens

Upload the gff file of Species 1 Species Pvu.gff

Upload the gff file of Species 2 Species Mtr.gff

Paraat

Upload cds file test.pep

Upload homologs file test.cds

Upload pep file test.homologs

kaks calculator

Upload pep file Upload kaks source file

Dupgen finder

Target species gene position file Ath.gff

Blast output file Ath.blast

Target and outgroup species gene position file Ath_Nnu.gff

Target and outgroup Blast output file Ath_Nnu.blast

Correspondence mc

Upload BLAST file: Ath.gff

Upload block file: Ath.blast

Upload Correspondence file: Ath_Nnu.gff

Species 1 lens file: Ath_Nnu.blast

Species 2 lens file: Ath_Nnu.blast

Species 1 gff file: Ath_Nnu.blast

Species 2 gff file: Ath_Nnu.blast

Gene retention

Upload mc file: mc file

Gene fractionation

Upload mc file: mc file

P-index

Upload mc file: mc file

Hmmer

Build HMM model comparison file: HMM model

Sequence database file: database file

pfam

Upload protein sequence file: protein file

meme

Upload the target database in FASTA format: FASTA file

cpgfinder

Upload nucleic acid file: nucleic file

codonw

Upload the sequence file: sequence file

gsds

Upload the sequence file: sequence file

Paraat

Upload cds file test.pep

Upload homologs file test.cds

Upload pep file test.homologs

kaks calculator

Upload pep file Upload kaks source file

Sequence_screening

Upload pep file Upload kaks source file

File_merge

Upload pep file Upload kaks source file

Find_alternative

Upload pep file Upload kaks source file

Extract_column

Upload pep file Upload kaks source file

Duplicate_removal

Upload pep file Upload kaks source file

Format_conversion

Upload pep file Upload kaks source file