... | ... | @@ -40,7 +40,7 @@ By default sequence data is kept on a single line. For a more readable output, y |
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## Supermatrix <a name="supermatrix"></a>
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In addition to individual alignments, a _supermatrix_ is also created by concatenating all the individual alignments together into a single file called `supermatrix.fas` (the filetype extension depends on your input alignments, so it might as well be called `supermatrix.fasta`, for example). The range of individual gene partitions are written to the file `gene_partitions.txt`. The output is similar to what you would get if you ran the individual output alignments through a alignment concatenator such as [FasconCAT](https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat). Missing data is denoted by either a ('N') or a ('X'), depending on the type of data (nucleotides or amino acids). The program will automatically guess whether the data consists of nucleotides or amino acids, based on unique characters _or_ by the amount of As, Cs, Gs, and Ts (if these characters make up more than 50% of all individual bases, then nucleotides are assumed).
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In addition to individual alignments, a _supermatrix_ is also created by concatenating all the individual alignments together into a single file called `supermatrix.fas` (the filetype extension depends on your input alignments, so it might as well be called `supermatrix.fasta`, for example). The range of individual gene partitions are written to the file `gene_partitions.txt`. The output is similar to what you would get if you ran the individual output alignments through a alignment concatenator such as [FasconCAT](https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat). Missing data is denoted by either a ('N') or a ('X'), depending on the type of data (nucleotides or amino acids). The program will automatically guess whether the data consists of nucleotides or amino acids, based on unique characters _or_ by the amount of A, C, G, or T-characters (if these characters make up more than 50% of all individual bases, then nucleotides are assumed).
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![supermatrix](uploads/414cf2e7cada6f961ae8691306e9ba99/supermatrix.png)
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