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[求助]
初次接触生物信息学 文献有些理解不了 希望各位帮帮忙！万分感谢！
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The OrthoMCL method was used to construct sets of orthogroups. Amino acid alignments for each orthogroup were generated with MUSCLE, and then trimmed by removing poorly aligned regions with trimAl 1.2, using the heuristic automate1 option . In order to sort and align transcriptome data into our eight-genome scaffold for downstream phylogenetic analyses,we first used ESTScan [69] to find the best reading frame for all unigenes. The best hit from a blast search against the inferred proteins of our eight-genome scaffold was then used to assign each unigene to an orthogroup. Additional sorted unigene sequences for the orthogroups of sequenced genomes were aligned at the amino acid level into the existing full alignments of eight sequenced species using ClustalX 1.8. Then these large alignments were trimmed again using trimAl 1.2 with the same settings. Each unigene sequence was checked and removed from the alignment if the sequence contained less than 70% of the total alignment length. Corresponding DNA sequences were then forced onto the amino acid alignments using custom Perl scripts, and DNA alignments were used in subsequent phylogenetic analysis. Maximum likelihood analyses were conducted using RAxML version 7.2.1, searching for the best maximum likelihood tree with the GTRGAMMA model by conducting 100 bootstrap replicates. 这是构建系统树 进行系统分析的步骤，希望能用简单易懂的方式帮我解释一下，非常非常非常感谢!!! |
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