scripts/MEGAsettings.txt
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_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_all/_A_MSA-bioinfo/

SEEK ID: https://fairdomhub.org/data_files/5858?version=1

Filename: scripts/MEGAsettings.txt

Format: Plain text document

Size: 697 Bytes

MEGA version 10.0.5

Alignment:

Align with MUSCLE, default settings (-2.9 Gap Open, 0.00 Gap Extend, 1.20 Hydrophobicity Multiplier, 2048 Max Memory in MB, 16 Max Iterations, UPGMA Cluster Method (Iterations 1,2), UPGMA Cluster Method (Other Iterations), 24 Min Diag Length (Lambda))



Phylogenetic tree:

Statistical Method: Maximum Likelihood
Test of Phylogeny: None (or Bootstrap method with 500 replications)
Substitution Model/Method: LG model
Rates among Sites: Uniform Rates
Gaps/Missing Data Treatment: Use all sites
ML Heuristic Method: Nearest-Neighbor-Interchange(NNI)
Initial tree for ML: Make initial tree automatically (Deafult - NJ/BioNJ)
Branch Swap Filter: None

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