Table 1 Comparisons of topologies, branch lengths, and internal branch support values between inferred phylogenies across two replicates.

From: An investigation of irreproducibility in maximum likelihood phylogenetic inference

Data set	Program	Coalescent-based ASTRAL species phylogenies (Run1 vs. Run2)			Concatenation-based ML species phylogenies (Run1 vs. Run2)
Data set	Program	Tree distance (%)^a	Branch distance^b	Bipartitions with different support values (%)^c	Tree distance (%)^a	Branch distance^b	Bipartitions with different support values (%)^c
Animal: Bees	IQ-TREE	22.5	NA	NA	0.0	1.46138E−07	2.7
Animal: Birds	IQ-TREE	1.5	NA	NA	0.0	4.09E−09	1.5
Animal: Butterflies	IQ-TREE	4.4	NA	NA	0.0	0.000283233	16.7
Animal: Lizards	IQ-TREE	3.8	NA	NA	0.0	1.49E−07	0.0
Animal: Marine fishes	IQ-TREE	6.8	NA	NA	0.0	1.03E−08	0.9
Animal: Rodents	IQ-TREE	0.0	NA	8.8	0.0	2.83E−10	0.0
Plant: Cardueae	IQ-TREE	4.9	NA	NA	0.0	2.45E−10	0.0
Plant: Caryophyllales	IQ-TREE	0.0	NA	0.0	0.0	0.0	0.0
Plant: Green plants	IQ-TREE	1.8	NA	NA	0.0	0.0	NA
Plant: Jaltomata	IQ-TREE	0.0	NA	0.0	0.0	8.00E−10	0.0
Plant: Protea	IQ-TREE	14.5	NA	NA	0.0	3.46E−10	0.0
Fungi: Aspergillaceae	IQ-TREE	0.0	NA	0.0	0.0	1.48E−07	0.0
Fungi: Budding yeasts	IQ-TREE	0.0	NA	1.8	0.0	0.0	0.0
Fungi: Hanseniaspora	IQ-TREE	0.0	NA	0.0	0.0	0.0	0.0
Fungi: Rhizoplaca	IQ-TREE	10.7	NA	NA	0.0	3.32E−10	0.0
Animal: Bees	RAxML-NG	8.6	NA	NA	0.0	0.0	0.0
Animal: Birds	RAxML-NG	1.5	NA	NA	0.0	0.0	0.0
Animal: Butterflies	RAxML-NG	2.0	NA	NA	0.0	0.0	0.0
Animal: Lizards	RAxML-NG	0.0	NA	30.8	0.0	0.0	0.0
Animal: Marine fishes	RAxML-NG	4.3	NA	NA	0.0	0.0	0.0
Animal: Rodents	RAxML-NG	0.0	NA	5.9	0.0	0.0	0.0
Plant: Cardueae	RAxML-NG	8.5	NA	NA	0.0	0.0	0.0
Plant: Caryophyllales	RAxML-NG	16.3	NA	NA	0.0	0.0	0.0
Plant: Green plants	RAxML-NG	0.7	NA	NA	0.0	0.0	0.0
Plant: Jaltomata	RAxML-NG	0.0	NA	8.3	0.0	0.0	0.0
Plant: Protea	RAxML-NG	21.0	NA	NA	0.0	0.0	0.0
Fungi: Aspergillaceae	RAxML-NG	0.0	NA	0.0	0.0	0.0	0.0
Fungi: Budding yeasts	RAxML-NG	0.0	NA	0.9	0.0	0.0	NA
Fungi: Hanseniaspora	RAxML-NG	0.0	NA	0.0	0.0	0.0	0.0
Fungi: Rhizoplaca	RAxML-NG	3.6	NA	NA	0.0	0.0	0.0

For each data set, coalescent-based ASTRAL trees were reconstructed from the Run1 and Run2 sets of individual gene trees; both Run1 and Run2 used identical settings, including substitution model, random starting seed number, number of threads of execution, number of independent tree searches, and ML program; concatenation-based ML trees were inferred twice from the supermatrix using IQ-TREE and RAxML-NG with identical settings.
^aPercentage of bipartitions (or internal branches) that differ between two inferred species trees was quantified the normalized Robinson–Foulds tree distance.
^bBranch distance between two inferred species trees was computed by the branch score distance of Kuhner and Felsenstein with the R packages ape and phangorn.
^cThe percentage of bipartitions (or internal branches) that received different bootstrap support values between two inferred species trees that were topologically identical (i.e., tree distance is 0). When topologies, branch lengths, or internal branch support values between two inferred phylogenies are identical, their estimated values are zero and are shown in bold. “NA” denotes “not applicable” due to either lack of external branch lengths in a coalescent-based ASTRAL tree, different topologies between two inferred species trees, or lack of standard bootstrap support values in the RAxML-NG analyses of the two largest data sets (plant: green plants and fungi: budding yeasts) due to computation cost.

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Table 1 Comparisons of topologies, branch lengths, and internal branch support values between inferred phylogenies across two replicates.

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