Data file: 59_Sciomyzidae_Aquatic2_constrained.phy [data set in phylip format] These files are readable by raxmlHPC-PTHREADS.iMAC and is set to conduct a 20-replicate RAxML analysis under the GTRGAMMAI model. The data set is partitioned by gene and codon position where applicable. Aquatic snail-feeding Tetanocera are constrained to be monophyletic except T. plumosa which can also be found on the shoreline. Make text file named Partitioning_59_Scio_RAxML.txt containing the following: DNA, COI_3rd = 1-1474\3 DNA, COI_1st = 2-1474\3 DNA, COI_2nd = 3-1474\3 DNA, COII_1st = 1475-2155\3 DNA, COII_2nd = 1476-2155\3 DNA, COII_3rd = 1477-2155\3 DNA, 28S = 2156-3250 DNA, 16S = 3251-3676 DNA, Ef1a_1st = 3677-4552\3 DNA, Ef1a_2nd = 3678-4552\3 DNA, Ef1a_3rd = 3679-4552\3 Make text file named Aquatic2_Constrained_59_Scio.txt containing the following: (Drosophila_melanogaster_AJ400907_M21017, Atrichomelina_pubera_161, Anticheta_melanosoma_254, Hoplodictya_acuticornis_277, Limnia_bosci_120, Tetanocera_arrogans_93, Tetanocera_clara_57, Tetanocera_elata_245, Tetanocera_elata_247, Tetanocera_fuscinervis_53, Tetanocera_fuscinervis_54, Tetanocera_fuscinervis_153, Tetanocera_hyalipennis_127, Tetanocera_hyalpennis_191, Tetanocera_hyalpennis_192, Tetanocera_kerteszi_46, Tetanocera_kerteszi_47, Tetanocera_melanostigma_2, Tetanocera_oxia_204, Tetanocera_phyllophora_39, Tetanocera_plebeja_1, Tetanocera_plebeja_13, Tetanocera_plebeja_205, Tetanocera_plumosa_11, Tetanocera_plumosa_43, Tetanocera_rotundicornis_206, Tetanocera_silvatica_172, Tetanocera_silvatica_173, Tetanocera_silvatica_35, Tetanocera_valida84,(Tetanocera_annae_201, Tetanocera_annae_202, Tetanocera_annae_229, Tetanocera_bergi_159, Tetanocera_ferruginea_34, Tetanocera_ferruginea_158, Tetanocera_latifibula_144, Tetanocera_latifibula_146, Tetanocera_latifibula_147, Tetanocera_latifibula_149, Tetanocera_loewi_189, Tetanocera_loewi_226, Tetanocera_mesopora_40, Tetanocera_montana_142, Tetanocera_montana_143, Tetanocera_montana_170, Tetanocera_montana_171, Tetanocera_obtusifibula_275, Tetanocera_obtusifibula_276, Tetanocera_robusta_10, Tetanocera_robusta_16, Tetanocera_robusta_134, Tetanocera_robusta_137, Tetanocera_soror_209, Tetanocera_soror_210, Tetanocera_vicina_94, Tetanocera_vicina_95, Tetanocera_vicina_98, Tetanocera_vicina_99)); These terminal commands will run this analysis if RAxML folder is on the computer Desktop and the data files are in this folder: cd Desktop/raxml ./raxmlHPC-PTHREADS.iMAC -T 2 -f d -s 59_Sciomyzidae_Aquatic2_constrained.phy -q Partitioning_59_Scio_RAxML.txt -g Aquatic2_Constrained_59_Scio.txt -n Aquatic2_Constrained_59_Scio.txt -m GTRGAMMAI -#20