Commandline Reference¶

General¶

-i [file or path]¶

Specify input file in normal, gunzip, or tar.gz, or a path includes all needed input files.

-o [file or path]¶

Specify output path.

-em [email address]¶

Email address that you want receive potential information from web tools.

-standalone¶

Run standalone mode. (Only for standalone version)

-lite¶

Run lite mode. (Only for standalone version)

-test¶

Run test mode.

-redo¶

Skip manually confirm for check point checking, automatically rerun the full pipeline.

-remake¶

According to exsisting output file, remake the tree image only.

Parse FASTA¶

-dh¶

Keep duplicate headers.

-tax¶

Search for taxonomy information for each sequence in Entrenz database.

-name¶

Search for protein name for each sequence in Entrenz database.

-pfam¶

Run Pfamsacn (domain prediction) for each sequence and then annotate protein domians on the tree.

-pev [E-value]¶

E-value of Pfamscan search.

Avaliable E-value:

50
20
10
5
2
1
0.1
0.01
0.001
0.0001
1e-5
1e-10
1e-50
1e-100
1e-300

Make alignment¶

-mafft¶

Enable MAFFT

-matrix¶

Score matrix for align sequences.

Avaliable Matrix:

bl30
bl45
bl62
bl80
jtt100
jtt200

-op¶

Gap Open penalty.

-ep¶

Gap extension penalty.

-retree¶

Tree rebuilding number.

Avaliable Value:

0
1
2
5
10
20
50
80
100 (long run)

-maxiterate¶

Maximum number of iterations to perform when refining the alignment.

Avaliable Value:

0
1
2
5
10
20
50
80
100 (long run)

-ffts¶

Perform fast fourier transform.

Avaliable Mode:

localpair
globalpair
genafpair

MUSCLE¶

-muscle¶

Enable muscle.

trimAl¶

-trimal¶

Enable trimal.

-tmod¶

trimal run mode.

Avaliable Mode:

automated1
gappyout
strict
strictplus

-rmss¶

Remove spurious sequences (residue overlap/sequence overlap).

Residue overlap means the minimum overlap of a positions with other positions in the column to be considered a “good position”.

Sequence overlap means the minimum percentage of “good positions” that a sequence must have in order to be conserved.

Make phylogenetic tree¶

-iqtree¶

Enable iqtree.

-iqmod¶

Run mode of iqtree.

Avaliable Mode:

TEST
TESTNEW
One or more spicified models

-boots¶

Bootstrap number.

-rcluster¶

Specify the percentage for the relaxed clustering algorithm to speed up the computation instead of the default slow greedy algorithm.

-mtree¶

Turn on full tree search for each model considered, to obtain more accurate result.

-bnni¶

Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments.

Tree Annotating¶

-xzoom¶

Horizontal magnification, default is 1.

-yzoom¶

Vertical magnification, default is 1.

-bs¶

Show bootstrap support value.

-bl¶

Show genomic distance value.

-bif¶

Show bifurcate number.

-leg¶

Generate domain legend.

-reroot¶

Reroot the tree.

-marktax¶

Color branches according to taxonomy.

-format¶

Output image format.

Avaliable Type:
png
pdf
svg