ClonalTree

Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances

ClonalTree is a new algorithm to reconstruct BCR lineage trees that incorporates genotype abundance into a minimum spanning tree to infer maximum parsimony trees.

CONTACT
E-mail: juliana.silva_bernardes@sorbonne-universite.fr

Inputs

• The alignment of clonally related BCR heavy chain sequences in FASTA format. The naive B cell heavy chain sequence must be included in the alignment, named as "naive". There are ways to provide the genotype abundance for each sequence :
  • By the sequence ID repetition in the alignment, or
  • By integrating the abundance of each sequence in its ID, for instance, the sequence Seq1 with an abundance of 6 will have the following ID:

    Seq1@6

• See example input files

Outputs

• ClonalTree returns:

  • [repertoire_name].nk : the reconstructed BCR lineage tree in newick format

  • [repertoire_name].nk.csv : a table in csv format, containing the parent relationship and cost.

• See example output files

Requirements

• numpy :

  $ conda install numpy
  

  or

  $ pip install numpy
  

• Biopython

  $ pip install biopython
  

• ete3 :

  $ pip install ete3
  

• networkx (for the evaluation) :

  $ pip install networkx
  

Using ClonalTree

The command line for launching the ClonalTree is:

$ python clonalTree.py  -i [seq_alignment_file] -o [output_newick_file] [...options]

required arguments

• [seq_alignment_file] is alignment of clonally related BCR heavy chain sequences in FASTA format,
• [output_newick_file] is output file name

optional arguments [...options]

• -a 1, if considering abundance, otherwise -a 0
• -r 1, if performing revision, otherwise -r 0
• -t 1, if performing trimming tree, otherwise -t 0

For instance the following command can be run in the src/ folder:

$ python src/clonalTree.py  -i Examples/input/simulation200.fasta -o Examples/output/clonalTree.abRT.nk -a 1 -r 1 -t 1

Output files will be placed as such:

~Examples/output/[seq_alignment_file].nk
                [seq_alignment_file].nk.csv

[seq_alignment_file] is the multiple sequence alignement of clonaly-related B cell receptor heavly chain seuqneces.

License, Patches, and Ongoing Developements

• The program is distributed under the CeCILL licence
• Feature requests and open issues.

Reference

Nika Abdollahi, Anne Langlois De Septenville, Frederic Davi and Juliana S. Bernardes. Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances. BMC Bioinformatics (2023): 24(1) 70