actledge

I have met the same problem T_T Is it possible to know what the cause of this is.

emmm, it seems that ,figtree generate the same order of branches with phandango. So I Just color the branches in figtree, And to combine the figures use AI. But I...

Does this mean that for a sequence of 2kbp, it would take 400 k-mers, and for a sequence of 20kbp, it would take 4000 k-mers if I set --kmer-per-seq-scale 0.2?...

These are outputs of each run: [linclust_default.txt](https://github.com/soedinglab/MMseqs2/files/14850149/linclust_default.txt) [linclust_kmer2000_clustmode1.txt](https://github.com/soedinglab/MMseqs2/files/14850150/linclust_kmer2000_clustmode1.txt) [linclust_kmerscale0.2_clustmode1.txt](https://github.com/soedinglab/MMseqs2/files/14850151/linclust_kmerscale0.2_clustmode1.txt) [linclust_kmerscale1_clustmode1.txt](https://github.com/soedinglab/MMseqs2/files/14850152/linclust_kmerscale1_clustmode1.txt) [linclust_kmerscale20_clustmode1.txt](https://github.com/soedinglab/MMseqs2/files/14850153/linclust_kmerscale20_clustmode1.txt) > This is surprising. For a 2k long sequence it should generate 420 k-mers (20 base + 0.2 *...

Uh, I have the same question.