# PhyloPhlAn **URL:** https://forum.biobakery.org/c/microbial-community-profiling/phylophlan/13.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the PhyloPhlAn category](https://forum.biobakery.org/t/about-the-phylophlan-category/27)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
Name: PhyloPhlAn User manual || Tutorial Description: PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipelin… --- ## [Phylophlan Discard a few mags](https://forum.biobakery.org/t/phylophlan-discard-a-few-mags/9053)
**Author:** [@Skylady](https://forum.biobakery.org/u/Skylady)\ **Replies:** 1\ **Last updated:** [September 10, 2026, 7:17am UTC](https://forum.biobakery.org/t/phylophlan-discard-a-few-mags/9053 "2026-09-10T07:17:40Z")
Hi! I tried to use PhyloPhlAn version 3.2.1 (13 February 2026) for MAGs, and saw that output file don’t have two MAGs, they are totally gone I have checked in each folder of tmp. In log file I have 152 as input files, … --- ## [Analysis taking too much time](https://forum.biobakery.org/t/analysis-taking-too-much-time/9023)
**Author:** [@Rishav\_Sahil](https://forum.biobakery.org/u/Rishav_Sahil)\ **Replies:** 3\ **Last updated:** [August 18, 2026, 12:20pm UTC](https://forum.biobakery.org/t/analysis-taking-too-much-time/9023 "2026-08-18T12:20:31Z")
Hello all, I am using this command phylophlan -i /mnt/bigdata/nikhil/Bradyrhizobium\_genomes -d phylophlan --databases\_folder /mnt/bigdata/nikhil/Bradyrhizobium\_genomes/database --diversity medium --configs\_folder /mnt/b… --- ## [How long does it usually take to build a phylogenetic tree with PhyloPhlAn 3 using about 30 genomes?](https://forum.biobakery.org/t/how-long-does-it-usually-take-to-build-a-phylogenetic-tree-with-phylophlan-3-using-about-30-genomes/8714)
**Author:** [@dwenchao234](https://forum.biobakery.org/u/dwenchao234)\ **Replies:** 2\ **Last updated:** [August 16, 2026, 8:41pm UTC](https://forum.biobakery.org/t/how-long-does-it-usually-take-to-build-a-phylogenetic-tree-with-phylophlan-3-using-about-30-genomes/8714 "2026-08-16T20:41:13Z")
This is my first time using PhyloPhlAn 3. I used the command below to build a tree for about 30 genomes, and the program has been running for over six days without finishing. The log files stopped showing any new output … --- ## [Missing dependency pyrodigal in bioconda recipe/biocontainers](https://forum.biobakery.org/t/missing-dependency-pyrodigal-in-bioconda-recipe-biocontainers/8907)
**Author:** [@alexhbnr](https://forum.biobakery.org/u/alexhbnr)\ **Replies:** 1\ **Last updated:** [June 10, 2026, 8:01am UTC](https://forum.biobakery.org/t/missing-dependency-pyrodigal-in-bioconda-recipe-biocontainers/8907 "2026-06-10T08:01:26Z")
Hello everyone, When trying to run phylophlan\_assign\_sgbs with the latest biocontainers image docker:// \`\`quay.io/biocontainers/phylophlan:3.2.1--pyhdfd78af\_1, I get an error message that pyrodigal cannot be executed. T… --- ## [FastTreeMP execution error](https://forum.biobakery.org/t/fasttreemp-execution-error/8342)
**Author:** [@Anahid\_Amani](https://forum.biobakery.org/u/Anahid_Amani)\ **Replies:** 0\ **Last updated:** [August 4, 2025, 8:30pm UTC](https://forum.biobakery.org/t/fasttreemp-execution-error/8342 "2025-08-04T20:30:10Z")
Hi there. Iwas wondering if I could get some help on this error I’m getting. I’ve run phylophal version 3.1.68, installed in a separate environment. the fir 2 runs were succesfull and now for my other MAGs and their cor… --- ## [Ethiopian tutorial error](https://forum.biobakery.org/t/ethiopian-tutorial-error/7920)
**Author:** [@Eun](https://forum.biobakery.org/u/Eun)\ **Replies:** 1\ **Last updated:** [July 2, 2025, 10:34am UTC](https://forum.biobakery.org/t/ethiopian-tutorial-error/7920 "2025-07-02T10:34:26Z")
Hello, I’m trying phylophlan tutorial. However, in the Ethiopian cohort part (Example 03), I’ve got an error. $ phylophlan\_assign\_sgbs -i input\_metagenomic -o output\_metagenomic --nproc 4 -n 1 -d ethoipia\_tutorial --da… --- ## [Can't download the Ethiopian genome bins（Ethiopian MAGs））](https://forum.biobakery.org/t/cant-download-the-ethiopian-genome-bins-ethiopian-mags/8202)
**Author:** [@langford](https://forum.biobakery.org/u/langford)\ **Replies:** 0\ **Last updated:** [June 30, 2025, 9:25am UTC](https://forum.biobakery.org/t/cant-download-the-ethiopian-genome-bins-ethiopian-mags/8202 "2025-06-30T09:25:53Z")
In " PhyloPhlAn 3 Example 03 Metagenomic application"(PhyloPhlAn 3 Example 03 Metagenomic application · biobakery/biobakery Wiki · GitHub), I need download the Ethiopian genome bins according to Step 1, because the link … --- ## [How to skip alignment step and use pre-aligned core genes for phylogeny?](https://forum.biobakery.org/t/how-to-skip-alignment-step-and-use-pre-aligned-core-genes-for-phylogeny/8203)
**Author:** [@shizhun](https://forum.biobakery.org/u/shizhun)\ **Replies:** 0\ **Last updated:** [June 30, 2025, 2:52pm UTC](https://forum.biobakery.org/t/how-to-skip-alignment-step-and-use-pre-aligned-core-genes-for-phylogeny/8203 "2025-06-30T14:52:50Z")
I’ve already generated a concatenated alignment file (genomes\_concatenated.aln) of core genes for my genomes using an external tool. I’d like to use PhyloPhlAn to directly build a phylogenetic tree from this alignment, s… --- ## [Unable to run example 1](https://forum.biobakery.org/t/unable-to-run-example-1/3870)
**Author:** [@quispe](https://forum.biobakery.org/u/quispe)\ **Replies:** 7\ **Last updated:** [June 23, 2025, 7:19pm UTC](https://forum.biobakery.org/t/unable-to-run-example-1/3870 "2025-06-23T19:19:30Z")
Hello! I’ve installed phylophlan by running the command: conda create -n “phylophlan” -c bioconda phylophlan=3.0. I then ran: ‘conda activate phylophlan’ and ‘phylophlan\_write\_default\_configs.sh \[output\_folder\]’. This… --- ## [Phylophlan questions](https://forum.biobakery.org/t/phylophlan-questions/8157)
**Author:** [@eo24a](https://forum.biobakery.org/u/eo24a)\ **Replies:** 0\ **Last updated:** [June 19, 2025, 12:41am UTC](https://forum.biobakery.org/t/phylophlan-questions/8157 "2025-06-19T00:41:11Z")
Hi, I am having hard time getting phylophlan work. I really need some fundamental help and where to obtain reference SGBs and genomes. So, I have metagenome bowtie2 files from metaphlan output. first question, can I us… --- ## [\[e\] gene\_markers\_identification crashed](https://forum.biobakery.org/t/e-gene-markers-identification-crashed/8156)
**Author:** [@eo24a](https://forum.biobakery.org/u/eo24a)\ **Replies:** 0\ **Last updated:** [June 18, 2025, 9:28pm UTC](https://forum.biobakery.org/t/e-gene-markers-identification-crashed/8156 "2025-06-18T21:28:47Z")
I have fasta files concatenated after cleaned up with kneaddata and I would like to develop a phylogenetic tree based on known reference genomes. At first i started with phylophlan. here are my parameters: phylophlan -i… --- ## [\[e\] No alignments found to concatenate](https://forum.biobakery.org/t/e-no-alignments-found-to-concatenate/4931)
**Author:** [@JWKANG](https://forum.biobakery.org/u/JWKANG)\ **Replies:** 4\ **Last updated:** [June 13, 2025, 7:04pm UTC](https://forum.biobakery.org/t/e-no-alignments-found-to-concatenate/4931 "2025-06-13T19:04:42Z")
PhyloPhlAn version 3.0.67 Hello, I have run my code as below. But I got an error message. \[e\] No alignments found to concatenate. Could you please let me know what is the issue here? I have attached the log file. T… --- ## [PhyloPhlAn in Galaxy: Requesting test database for phylophlan\_assign\_sgbs](https://forum.biobakery.org/t/phylophlan-in-galaxy-requesting-test-database-for-phylophlan-assign-sgbs/8070)
**Author:** [@neo417](https://forum.biobakery.org/u/neo417)\ **Replies:** 0\ **Last updated:** [May 18, 2025, 2:10pm UTC](https://forum.biobakery.org/t/phylophlan-in-galaxy-requesting-test-database-for-phylophlan-assign-sgbs/8070 "2025-05-18T14:10:03Z")
Dear PhyloPhlAn Team, I am currently wrapping the PhyloPhlAn 3 tool suite for use in Galaxy. You can view my progress at https://github.com/neo417/galaxy-tools. Galaxy requires a tool wrapper to provide test data for v… --- ## [Phylophlan not considering all the MAGs for creation of .tre file](https://forum.biobakery.org/t/phylophlan-not-considering-all-the-mags-for-creation-of-tre-file/8023)
**Author:** [@alaloo](https://forum.biobakery.org/u/alaloo)\ **Replies:** 0\ **Last updated:** [April 25, 2025, 3:42am UTC](https://forum.biobakery.org/t/phylophlan-not-considering-all-the-mags-for-creation-of-tre-file/8023 "2025-04-25T03:42:49Z")
I would like to generate a phylogentic tree of 120 de-replicated MAGs of which 84 are bacteria and 36 are archaeal MAGs. However when we run all the 120 MAGs together I get only 101 MAGs on the RAxML\_bestTree.Genome\_pea… --- ## [Trouble with Arguments and Time it Takes to Make Tree](https://forum.biobakery.org/t/trouble-with-arguments-and-time-it-takes-to-make-tree/7861)
**Author:** [@Alex-A-B-C](https://forum.biobakery.org/u/Alex-A-B-C)\ **Replies:** 0\ **Last updated:** [February 24, 2025, 5:36pm UTC](https://forum.biobakery.org/t/trouble-with-arguments-and-time-it-takes-to-make-tree/7861 "2025-02-24T17:36:36Z")
Hello, I recently started using PhyloPhlAn. I have 500 strains of interest that I want to make the tree with. To do so I uploaded the nucelotide WGS sequences for them, and ran PhyloPhlAn. phylophlan \\ -i key\_genome… --- ## [Explanation of the output of phylophlan\_metagenomic](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588)
**Author:** [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\ **Replies:** 3\ **Last updated:** [February 10, 2025, 1:36pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588 "2025-02-10T13:36:17Z")
Hello! I am a bit confused about the output of phylophlan\_metagenomic. For example, I have run it with a novel MAG and it gives me: uSGB\_48157:Family:k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Actinobacteria|o\_\_Geodermatophilale… --- ## [Result of phylophlan\_assign\_sgbs resulting in error in phylophlan\_draw\_metagenomic?](https://forum.biobakery.org/t/result-of-phylophlan-assign-sgbs-resulting-in-error-in-phylophlan-draw-metagenomic/7774)
**Author:** [@LPrunus](https://forum.biobakery.org/u/LPrunus)\ **Replies:** 0\ **Last updated:** [January 28, 2025, 10:27am UTC](https://forum.biobakery.org/t/result-of-phylophlan-assign-sgbs-resulting-in-error-in-phylophlan-draw-metagenomic/7774 "2025-01-28T10:27:28Z")
Dear all, I’m trying to follow the Phylophlan tutorials with my own data and I ran into a problem while trying to use the phylophlan\_draw\_metagenomic function. phylophlan\_assign\_sgbs.py version 3.1.40 (6 March 2024) p… --- ## [Phylophlan: problem with bootstrap instructions in the config file](https://forum.biobakery.org/t/phylophlan-problem-with-bootstrap-instructions-in-the-config-file/7687)
**Author:** [@Patologia\_Vegetal](https://forum.biobakery.org/u/Patologia_Vegetal)\ **Replies:** 0\ **Last updated:** [December 22, 2024, 6:30pm UTC](https://forum.biobakery.org/t/phylophlan-problem-with-bootstrap-instructions-in-the-config-file/7687 "2024-12-22T18:30:30Z")
Phylophlan To construct a tree with Phylophlan, I am including instructions to perform bootstrap analysis directly in the config file, and I am writing this: \[tree2\] program\_name = /home/jesus/miniconda3/envs/phylo\_en… --- ## [No metabat\_bin is assigned by PhyloPhlan --- metabat\_bin.# is close to an SGB not present in the SGB.Jun23 database](https://forum.biobakery.org/t/no-metabat-bin-is-assigned-by-phylophlan-metabat-bin-is-close-to-an-sgb-not-present-in-the-sgb-jun23-database/7119)
**Author:** [@hoangphuctrinh](https://forum.biobakery.org/u/hoangphuctrinh)\ **Replies:** 3\ **Last updated:** [October 22, 2024, 4:13pm UTC](https://forum.biobakery.org/t/no-metabat-bin-is-assigned-by-phylophlan-metabat-bin-is-close-to-an-sgb-not-present-in-the-sgb-jun23-database/7119 "2024-10-22T16:13:59Z")
Hello, Thank you for the tool. However, I cannot get any species assignment when I run phylophlan\_assign\_sgbs. This is the result for phylophlan\_out.tsv #input\_bin \[u|k\]\[S|G|F\]GBid:taxa\_level:taxonomy:avg\_dist \[… --- ## [\[e\] gene\_markers\_selection crashed (SOLUTION)](https://forum.biobakery.org/t/e-gene-markers-selection-crashed-solution/7481)
**Author:** [@baldeguer-riquelme](https://forum.biobakery.org/u/baldeguer-riquelme)\ **Replies:** 0\ **Last updated:** [October 7, 2024, 7:11pm UTC](https://forum.biobakery.org/t/e-gene-markers-selection-crashed-solution/7481 "2024-10-07T19:11:54Z")
Hi, Thank you for developing this great tool! I was running PhyloPhlAn version 3.1.68 to create a phylogenomic tree using the command: phylophlan -i Protein\_files/ -o Phylogenomic\_tree/ -f supermatrix\_aa.cfg --diversi… --- ## [Error when running PhyloPhlAn \[e\] No alignments found to concatenate](https://forum.biobakery.org/t/error-when-running-phylophlan-e-no-alignments-found-to-concatenate/7414)
**Author:** [@brilliant2643](https://forum.biobakery.org/u/brilliant2643)\ **Replies:** 0\ **Last updated:** [August 28, 2024, 2:23pm UTC](https://forum.biobakery.org/t/error-when-running-phylophlan-e-no-alignments-found-to-concatenate/7414 "2024-08-28T14:23:23Z")
Hi! I’m using phylophlan version3.1.68 to construct a phylogenic tree from 68 MAGs files, but I got an error message: \[e\] No alignments found to concatenate I use this command to set the configuration file: phylophla… --- ## [Error phylophlan\_assign\_sgbs.py](https://forum.biobakery.org/t/error-phylophlan-assign-sgbs-py/7216)
**Author:** [@LisaCarraro](https://forum.biobakery.org/u/LisaCarraro)\ **Replies:** 3\ **Last updated:** [August 7, 2024, 4:24pm UTC](https://forum.biobakery.org/t/error-phylophlan-assign-sgbs-py/7216 "2024-08-07T16:24:46Z")
Hallo, I am using Phylophlan version 3.0.68. I receive this error : File “/usr/local/lib/python3.12/site-packages/phylophlan/phylophlan\_assign\_sgbs.py”, line 934, in phylophlan\_metagenomic bash: File: command not foun… --- ## [Phylophlan: error: unrecognized arguments: --strainphlan](https://forum.biobakery.org/t/phylophlan-error-unrecognized-arguments-strainphlan/6039)
**Author:** [@erica5](https://forum.biobakery.org/u/erica5)\ **Replies:** 5\ **Last updated:** [August 7, 2024, 4:16pm UTC](https://forum.biobakery.org/t/phylophlan-error-unrecognized-arguments-strainphlan/6039 "2024-08-07T16:16:38Z")
Hello, I’m trying to run StrainPhlan from (MetaPhlan version 4.1.0 (23 Aug 2023), installed via conda) using the following command: strainphlan -s consensus\_markers/\*.json.bz2 -m db\_markers/t\_\_SGB4608.fna -r reference… --- ## [PhyloPhlAn 3: Example 05: Proteobacteria ANI figure](https://forum.biobakery.org/t/phylophlan-3-example-05-proteobacteria-ani-figure/7296)
**Author:** [@Shaelyn](https://forum.biobakery.org/u/Shaelyn)\ **Replies:** 1\ **Last updated:** [August 7, 2024, 4:08pm UTC](https://forum.biobakery.org/t/phylophlan-3-example-05-proteobacteria-ani-figure/7296 "2024-08-07T16:08:41Z")
Hello there, I am wondering what program was used to generate the ANI heatmap next to the Proteobacteria phylogenetic tree. Thanks, Shaelyn --- ## [Phylogenetic tree for 2000 genomes](https://forum.biobakery.org/t/phylogenetic-tree-for-2000-genomes/7146)
**Author:** [@Jesse](https://forum.biobakery.org/u/Jesse)\ **Replies:** 2\ **Last updated:** [July 11, 2024, 10:51pm UTC](https://forum.biobakery.org/t/phylogenetic-tree-for-2000-genomes/7146 "2024-07-11T22:51:47Z")
Hello, I want to build a phylogenetic tree for ~2000 genomes with high diversity. I followed the tutorial but not sure what is the best way to do that with phylphlan 3.1.22. Based on the different examples, it seems t… --- ## [Questions about the command in Step1 of Example 02](https://forum.biobakery.org/t/questions-about-the-command-in-step1-of-example-02/7207)
**Author:** [@brilliant2643](https://forum.biobakery.org/u/brilliant2643)\ **Replies:** 1\ **Last updated:** [July 11, 2024, 3:39pm UTC](https://forum.biobakery.org/t/questions-about-the-command-in-step1-of-example-02/7207 "2024-07-11T15:39:39Z")
Hi! I’m using PhyloPhlAn3 to construct phylogenic tree from my genomes. I followed the instruction of example2 in GitHub, but came across some problems. After I run step1 command, I found that the command seemed not to … --- ## [How to use GTDB database using phylophlan](https://forum.biobakery.org/t/how-to-use-gtdb-database-using-phylophlan/5698)
**Author:** [@pragya\_kohli](https://forum.biobakery.org/u/pragya_kohli)\ **Replies:** 3\ **Last updated:** [July 11, 2024, 3:35pm UTC](https://forum.biobakery.org/t/how-to-use-gtdb-database-using-phylophlan/5698 "2024-07-11T15:35:51Z")
I want to use GTDB database (manually downloaded) with phylophlan. Kindly guide me through the steps. --- ## [Phylophlan-3.1.1 :: setup.py miss requests in requirements](https://forum.biobakery.org/t/phylophlan-3-1-1-setup-py-miss-requests-in-requirements/6947)
**Author:** [@EricDeveaud](https://forum.biobakery.org/u/EricDeveaud)\ **Replies:** 0\ **Last updated:** [April 22, 2024, 3:09pm UTC](https://forum.biobakery.org/t/phylophlan-3-1-1-setup-py-miss-requests-in-requirements/6947 "2024-04-22T15:09:14Z")
Hello fresh install of phylophlan-3.1.1 from tagged version https://github.com/biobakery/phylophlan/archive/refs/tags/3.1.1.tar.gz in a virtual env with python/3.8.1 phylophlan\_setip\_database --help exit with the follo… --- ## [Phylophlan arcahea clustering within bacteria](https://forum.biobakery.org/t/phylophlan-arcahea-clustering-within-bacteria/6699)
**Author:** [@mrgambero](https://forum.biobakery.org/u/mrgambero)\ **Replies:** 4\ **Last updated:** [April 10, 2024, 5:11pm UTC](https://forum.biobakery.org/t/phylophlan-arcahea-clustering-within-bacteria/6699 "2024-04-10T17:11:39Z")
Hello biobackery developers and thanks very much for your amazing work you do. I have a question for you. I binned some MAGs from some metagenomic data I have and I used phylophlan to reconstruct a phylogenetic tree amo… [Next page](https://forum.biobakery.org/c/microbial-community-profiling/phylophlan/13.md?page=1)