PLAZA 4.5 PLAZA 4.0 PLAZA 3.0 PLAZA 2.5 PLAZA 1.0

Construction settings

Setting for the tools used to generate the platform (in alphabetical order). Links to either the official website or to the relevant publication are provided.

Gene family construction settings

BLAST

Reference: Altschul et al.

  • E-value threshold 1e-05
  • retaining the best 1250 hits

DIAMOND

Reference: Huson et al.

  • E-value threshold 1e-05
  • retaining the best 1250 hits

TribeMCL

Source: Official website

  • mclblastline
  • I = 2
  • scheme = 4
  • other parameters are left on their default values

OrthoMCL 1.4

Source: Official website

  • default settings

OrthoMCL 2.0

Source: Official website

  • default settings

OrthoFinder

Source: Official website

  • Default settings, using DIAMOND output as input

Phylogeny construction settings

ClustalW

Source: Official website

  • Default settings

FastTree

Source: Official website

  • default settings

MUSCLE

Source: Official website

  • Default settings

Notung

Source: Official website

  • Default settings

PhyML

Source: Official website

  • Default parameters for protein sequences

Colinearity construction settings

i-ADHoRe 2.x

Source: Official website i-ADHoRe 2.0

  • alignment_method: gg
  • gap_size: 30
  • cluster_gap: 35
  • q_value: 0.85
  • prob_cutoff: 0.01
  • anchor_points: 5
  • level_2_only: false

i-ADHoRe 3.0

Source: Official website i-ADHoRe 3.0

  • alignment_method: gg
  • gap_size: 30
  • cluster_gap: 35
  • q_value: 0.85
  • prob_cutoff: 0.01
  • anchor_points: 5
  • level_2_only: false

PAML

Source: Official website

  • verbose: 0
  • noisy: 0
  • runmode: -2
  • seqtype: 1
  • model: 0
  • NSsites: 0
  • icode: 0
  • fix_alpha: 0
  • fix_kappa: 0
  • RateAncestor: 0
  • CodonFreq: 2

Functional construction settings

C-Hunter

Reference : Yi et al.
Source: Official website

Multiple experiments can be performed per PLAZA instance, depending on a combination of the following settings/options

  • Data type (e.g. GO, InterPro)
  • Collapsing of tandem genes to the tandem representative (yes/no)
  • Minimum/maximum size of cluster
  • Minimum/maximum number of functionally related genes within a cluster
  • E-value cut-off