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Hi I use fastANI distance matrix, first converted to fastani.phylip using following code, ``` pairwise_identities_to_distance_matrix.py --max_dist 0.2 tree/fastani_output > tree/fastani.phylip ``` then creates a tree with ``` bionj_tree.R tree/distances.phylip tree/tree.newic...

Hi I use bionj_tree.R created a phylogeny tree. However, the tree has no branches length information. Is there a way to add branches length to the tree? Also, I don't...

Hi , Could any one please help me explain what does this visualization mean? the three contigs are connecting to each other by a black line, what does that black...

read_info_histogram.sh not running on my data

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I try to run read_info_histogram.sh, here is my command and output, (base) campus-025-033:agro_3rd dklabuser$ ./read_info_histogram.sh BC05.fastq READ SET SUMMARY ---------------- number of reads: 0 number of bases: 0 ./read_info_histogram.sh: line...

the output of read_info_histograms.sh is not right.

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HI [Kin002_nano_QC.txt](https://github.com/rrwick/Filtlong/files/4074060/Kin002_nano_QC.txt) I made read_info_histograms.sh work to check my nanopore long reads quality, and found that the output of the MEAN QUALITIES are not right. Could anyone please help me...

ggtree visualization different from dendroscope visualization

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### Prerequisites Hi, I created a phylogenetic tree from whole genome ANI values 0f 300 strains. When I visualized the tree using ggtree, it had polytomy branches while it was...

Hi I am trying to use roary_plots.py to visualize my phylogenetic tree, so I run the command following, however, there is an error saying: No module named 'matplotlib' . Does...

can fastANI generate an alignment of conserved regions used for calculating ANI values?

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Hi I ran fastANI and used the output.txt to generate a distance matrix, after that, a neighbour joining tree was created using bionj_tree.R. Feels like most people prefer ML tree...

install rpy2 failed "ld: library not found for -lpcre2-8" on Mac

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**Describe the issue or bug** I am using a Mac M2. Trying to install rpy2 through jupyter notebook running on Visual Studio Code. And it failed with the following error....

docker run failed on Mac

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Hi I tried running BraCer on my Mac using docker, here is my command: `docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer test -o test_data` However, I got the...