Table 1 A comparison of the features among EasyCGTree and other pipelines with similar functions
From: EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
Pipeline | EasyCGTree | autoMLST | bcgTree | GToTree | UBCG |
|---|---|---|---|---|---|
Operation system | Linux, Windows | Linux | Linux | Linux | Linux, Mac OS |
Lanuage | Perl | Java, Python | Java, Perl | Python | Java |
Additional module | None | None | Five Perl modules | None | None |
Package size | 17 MB (Linux); 20 MB (Windows) | ~ 25 GB | 17 MB | 140 KB (without HMMs) | 8 MB |
Prerequisites | Perl | conda, Python, git | git, Java, Perl | conda, Python | Java |
Pre-installed software | None* | hmmsearch, trimAl, ASTRAL, IQ-TREE, MAFFT, MASH, Prodigal, RaxML | hmmsearch, Gblocks, MUSCLE, Prodigal, RaxML | hmmsearch, trimAl, FastTree, MUSCLE, Prodigal, TaxonKit | hmmsearch, FastTree, MAFFT, Prodigal |
Default HMM | bac120 | Depends on bacterial family | essential | Not specified | UBCG |
HMM extensibility | Yes | No | Yes | Yes | No |
Input | Prot | Nucl | Nucl, prot | Nucl | Nucl |
Trimming | trimAl | trimAl | Gblocks | trimAl | None |
Alignment | MUSCLE or Clustal Omega | MAFFT | MUSCLE | MUSCLE | MAFFT |
Tree-making approach | SM, ST | SM, ST | SM | SM | SM |
Phylogeny inference | FastTree, IQ-TREE | IQ-TREE, RaxML | RaxML | FastTree | FastTree, RaxML |