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Table 1 LMAP_S listing of integrated software (31) and related stages

From: LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation

LMAP_S StageIntegrated SoftwareReferencesAlgorithms 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)[29, 75](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)[80, 81](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) (*)[85, 86]Default
RYcode (v.1.0.0) (*)This workDefault
Stage 6 (PCC)CONSEL (v.1.20)[87]Default (includes makermt, consel and catpv)
TreeCmp (v.1.1)[88]Default
  1. Legend: (Number) – Algorithms Implemented column, where present, indicates the total number of algorithms implemented. (n.f.) – not found. (*) – Integrated as part of Stage 5 IQ-TREE algorithms DNA (DEG) and DNA (RY). (#) – Stage 4 consensus algorithms. DNA (nucleotide coding), DEG (degeneracy coding), RY (puRine and pirYmidine coding), NT2AA (translated – amino acid coding). AIC (Akaike Information Criterion) [89], BIC (Bayesian Information Criterion) [90], NNI (Nearest-Neighbor Interchange), SPR (Subtree Prunning and Regrafting). dN (non-synonymous distance), dS (synonymous distance). Listed software versions (see also Additional file 2: Figure S7) are only for reference of working cases and can be replaced by newer ones