After a gene homology alignment has finished, you can view the results in the:
- Tree view — The phylogenetic tree was automatically calculated according to the algorithm you specified in the Assembly Output screen and is ready to view.
- Homologs view — This view contains two tables with customizable and detailed results of the alignment. A drop-down menu in the upper-left corner of the view lets you toggle between the tables.
In addition, useful tab-delimited text files are automatically created and stored in the output folder you specified in the Assembly Output screen. These files are described below:
| Folder | File or subfolder name | Description |
|---|---|---|
| Homolog Summary Tables | All_Found_Homologs_foundIn.txt | A raw data data table that provides a list of all found genes and one or more genomes that contain them. |
| All_Found_Homologs-geneTable.txt | A raw data table that provides a list of all found genes and the length, %similarity, and %coverage of each gene aligned to the reference gene. | |
| Genomes_Info.txt | A list of the input genome used in the alignment and analysis. | |
| Shared-by-All_Homologs.txt | A raw data table that provides a list of all found genes that occur in all genomes, as compared to the reference genome. | |
| Unique_to_Reference_genes.txt | A list of genes found only in the reference genome. | |
| Shared-by_All-Homologs-Proteins | Concatenated Proteins (folder) | This folder contains files for all translated proteins of all the Shared Homologs, concatenated into the same genomic order as they occur in the reference genome. |
| Unconcatenated Proteins (folder) | This folder contains files for all translated proteins of all the identified Shared Homologs. |
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