Table 1 LMAP_S listing of integrated software (31) and related stages
From: LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation
LMAP_S Stage | Integrated Software | References | Algorithms Implemented |
|---|---|---|---|
Stage 2 (AE) | Clustal Omega (v.1.2.1) | [61] | Default |
ClustalW (v.2.1) | [62] | Default | |
Dialign-tx (v.1.0.2) | [63] | (3) Dialign-tx Default; Dialign-tx -D option; Dialign-tx -T option | |
FSA (v.1.15.9) | [64] | (2) FSA Default; FSA with ‘nucprot’ option | |
GramAlign (v.3.0) | [65] | Default | |
Kalign (v.2.04) | [66] | Default | |
MACSE (v.1.0.2) | [67] | (2) MACSE Default, MACSE with pseudogene alignment | |
MAFFT (v.7.271) | [68] | (8) MAFFT Default, MAFFT with ‘auto’ option, MAFFT E-INS-I, MAFFT FFT-NS-1, MAFFT FFT-NS-2, MAFFT FFT-NS-I, MAFFT G-INS-I, MAFFT L-INS-I | |
MUSCLE (v.3.8.31) | [26] | Default | |
Opal (v.2.1.3) | [69] | Default | |
Prank (v.150803) | [27] | (6) Prank Default, Prank +F option, Prank ‘once’ option, Prank CODON, Prank CODON + F option, Prank CODON ‘once’ option. | |
ProbAlign (v.1.4) | [70] | Default | |
ProbCons (v.1.12) | [71] | Default | |
T-COFFEE (v.11.00.8cbe486) | [72] | (4) Default ‘PROBA_PAIR’, ‘T_COFFEE_MSA’, ‘KTUP_MSA’, ‘PLIB_MSA’ | |
Stage 3 (AOD) | OD-Seq (v.1.0) | [73] | Default |
EvalMSA (v.1.0) | [74] | Default | |
Stage 4 (ARC) | Gblocks (v.0.91b) | (2) Default DNA, Default CODON | |
MaxAlign (v.1.1) | [31] | Default | |
MergeAlign (n.f.) | [76] | Default (#) | |
Noisy (v.1.5.12) | [77] | Default | |
PSAR-Align (v.1.0) | [78] | Default | |
TCS (T-COFFEE) (v.11.00.8cbe486) | [79] | (3) TCS, TCS_original, TCS_FM | |
TrimAl (v.1.4) | [30] | (6) TrimAl Default, TrimAl ‘automated1’, TrimAl ‘gappyout’, TrimAl ‘strictplus’, TrimAl ‘strict’, TrimAl ‘compareset’ (#) | |
WeaveAlign (v.1.2.1) | [20] | Default (#) | |
Stage 5 (PE) | IQ-TREE (v.1.6.2) | (15) IQ-TREE DNA, IQ-TREE DNA (DEG), IQ-TREE DNA (RY), IQ-TREE CODON, IQ-TREE NT2AA. Each case is available for Default and Standard / UFBoot [81] Bootstraps | |
MPBoot (v.1.1.0) | [82] | (2) MPBoot DNA. Each case is available for Default and “UFBoot” Bootstraps | |
Ninja (v.1.2.2) | [83] | Default | |
SMS (v.1.8.1) | [84] | (4) AIC + NNI, AIC + SPR, BIC + NNI, BIC + SPR | |
Degen (v.1.4) (*) | Default | ||
RYcode (v.1.0.0) (*) | This work | Default | |
Stage 6 (PCC) | CONSEL (v.1.20) | [87] | Default (includes makermt, consel and catpv) |
TreeCmp (v.1.1) | [88] | Default |