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Table 7 Numbers of “bad” reconstructions

From: PQ, a new program for phylogeny reconstruction

Dataset

Threshold

PQ

ME

ML

MP

QP

Metazoa-10

0.571

193

239

248

317

210

Metazoa-15

0.5

320

375

402

487

333

Fungi-15

0.417

278

336

413

486

287

Proteobacteria-15

0.667

184

213

250

297

189

Metazoa-25

0.545

203

247

248

371

213

Fungi-30

0.518

223

235

297

355

212

Proteobacteria-30

0.778

173

210

252

290

197

Fungi-45

0.524

205

202

255

344

200

Proteobacteria-45

0.833

169

172

202

262

172

  1. The column “Threshold” contains third (higher) quartils of Robinson – Foulds distances between PQ trees and species trees, for each set. Numbers in other columns are numbers of trees reconstructed by each method whose distance to the corresponding species tree is greater than the threshold. Numbers in PQ column are less than 1/4 of total volumes of the sets because the distance can take only few possible values