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Table 5 Phylogenetic analysis of all contradicting GFC cluster and YGOB pillars

From: GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm

Pillars

Method

Dupl’s

Losses

D/L scores

# genes

Score per gene

YGOB pillars not found in GFC

YGOB

53

219

298.5

196

1.523

 

GFC

-

-

-

-

-

GFC clusters containing probable pillars

YGOB

-

-

-

-

-

 

GFC

68

269

371

306

1.212

YGOB pillars containing GFC clusters

YGOB

438

1837

2494

1321

1.888

 

GFC

367

1448

1998.5

1221

1.637

GFC clusters containing YGOB pillars

YGOB

43

164

228.5

126

1.813

 

GFC

58

210

297

188

1.580

  1. The phylogenetic quality of clusters formed by GFC-Average linkage clusters and alternatives suggested by YGOB is shown here. The pillars/clusters are of size ≥ 4 and includes pillars not clustered together by GFC and vice versa, GFC clusters contained in YGOB and probable pillar-like clusters (at most one member from each pre-WGD species and at most two members from each post-WGD species with at least one ortholog) that contain YGOB clusters. The numbers of genes in each cluster are summed up to find the total number of genes. NOTUNG’s D/L score divided by the total number of genes gives the average score per gene, where a lower ratio indicates a better fit according to the MPR