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Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements

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Comparative Genomics (RECOMB-CG 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13234))

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Abstract

Placing a new sequence onto an existing phylogenetic tree is increasingly used in downstream applications ranging from microbiome analyses to epidemic tracking. Most such applications deal with noisy data, incomplete references, and model misspecifications, all of which make the correct placement uncertain. While recent placement methods have increasingly enabled placement on ultra-large backbone trees with tens to hundreds of thousands of species, they have mostly ignored the issue of uncertainty. Here, we build on the recently developed distance-based phylogenetic placement methodology and show how the distribution of placements can be estimated per input sequence. We compare parametric and non-parametric sampling methods, showing that non-parametric bootstrapping is far more accurate in estimating uncertainty. Finally, we design and implement a linear algebraic implementation of bootstrapping that makes it faster, and we incorporate the computation of support values as a new feature in the APPLES software.

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Authors and Affiliations

  1. Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh

    Navid Bin Hasan, Avijit Biswas & Md. Shamsuzzoha Bayzid

  2. Bioinformatics and System Biology Program, UC San Diego, San Diego, CA, 92093, USA

    Metin Balaban & Siavash Mirarab

  3. Electrical and Computer Engineering, UC San Diego, San Diego, CA, 92093, USA

    Siavash Mirarab

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  1. Navid Bin Hasan
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  4. Siavash Mirarab
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  5. Md. Shamsuzzoha Bayzid
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Correspondence to Md. Shamsuzzoha Bayzid .

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  1. University of Saskatchewan, Saskatoon, SK, Canada

    Lingling Jin

  2. Carnegie Mellon University, Pittsburgh, PA, USA

    Dannie Durand

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Hasan, N.B., Biswas, A., Balaban, M., Mirarab, S., Bayzid, M.S. (2022). Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. In: Jin, L., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2022. Lecture Notes in Computer Science(), vol 13234. Springer, Cham. https://doi.org/10.1007/978-3-031-06220-9_3

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