Properties and phylogenies of individual marker genes
======

Database files:

 - fasttree/*.nwk: Individual gene trees inferred using FastTree.

   - They are not the ones inferred by uDance, which partitions the taxon set
     (see ../udance). Instead, they were inferred separately from the trimmed
     alignments. Each tree represents the entire taxon set where the gene was
     found. These trees are unrooted.

Procedures:

Phylogenetic reconstruction was performed using FastTree v2.1.11 with the LG+G
model on the trimmed alignments.

The FastTree executable was compiled to support double precision floating point
arithmetic, which is necessary for most trees in order to resolve short branch
lengths. Otherwise (see single/), some runs will encounter numeric errors.

Compile FastTree:

```
gcc -DUSE_DOUBLE -O3 -finline-functions -funroll-loops -Wall \
-o FastTree FastTree.c -lm
```

Build each gene tree:

```
FastTree -lg -gamma -seed 12345 input.fasta > output.nwk
```