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Table 2 Running times and RAM both phyBWT2 and SANS

From: phyBWT2: phylogeny reconstruction via eBWT positional clustering

Datasets

PhyBWT2

SANS

Preprocessing

Phylogeny

RAM

Wall clock

 

RAM (Kb)

Wall clock (hh:mm:ss)

RAM (Kb)

Wall clock (hh:mm:ss)

(Kb)

(hh:mm:ss)

 

12 yeasts

27,559,652

3:19:03

6752

3:12

2,779,692

35:58

 

Drosophila

92,536,548

26:11

9516

8:50

30,107,232

21:04

 

42 yeasts

47,696,220

(BCR+bwt2lcp) 08:06:08

1,874,388

01:26:17

14,128,724

32:48:43

(k=32)

 

4,461,196

(only BCR) 16:27:45

12,368,416

45:52:01

(k=25)

HIV-1

18,996

\(< 1\)s

8452

\(< 1\)s

9,020

\(< 1\)s

 

Ebolavirus

18,256

\(< 1\)s

8460

\(< 1\)s

9,112

\(< 1\)s

 

E. coli—Shigella

5,484,644

1:21

12,648

1:38

303,868

3:06

 
  1. We also show the the resources needed to build the data structures during the preprocessing using the tool BCR [15] and bwt2lcp [46] for short reads and gsufsort [45] for long sequences. All tools were run using one core only. The wall clock time and RAM usage are taken from the output of the /usr/bin/time command.
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Algorithms for Molecular Biology

ISSN: 1748-7188