I have been trying to create a heatmap using phyloFlash_heatmap.R, but with the samples clustered by phylogeny. I have generated a distance matrix based on 18S, and am attempting to use it as the base of the sample clustering using the following command:
rscript phyloFlash_heatmap.R --custom-distance-matrix-sample=custom_distance_matrix_for_heatmap.tsv --library-name-from-file --cluster-samples=custom --min-ntu-count=300 *.csv
For many groups, the clustering becomes identical. However, for several samples, the phyloflash clustering does not match the trees given to me by programs such as iqtree or T-rex when they are provided with the same distance matrix.
Am I not providing the distance matrix correctly, or does phyloflash use a different logic to build the tree compared to these other programs?
Hi,
I have been trying to create a heatmap using phyloFlash_heatmap.R, but with the samples clustered by phylogeny. I have generated a distance matrix based on 18S, and am attempting to use it as the base of the sample clustering using the following command:
rscript phyloFlash_heatmap.R --custom-distance-matrix-sample=custom_distance_matrix_for_heatmap.tsv --library-name-from-file --cluster-samples=custom --min-ntu-count=300 *.csvFor many groups, the clustering becomes identical. However, for several samples, the phyloflash clustering does not match the trees given to me by programs such as iqtree or T-rex when they are provided with the same distance matrix.Am I not providing the distance matrix correctly, or does phyloflash use a different logic to build the tree compared to these other programs?
Thanks! Arno
Iqtree:
T-rex server:
Phyloflash_heatmap.R:
