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--- phylogeny_protocol2 [2021/10/10 19:05] – 134.190.232.9
+++ phylogeny_protocol2 [2022/02/07 15:21] (current) – 134.190.232.106
@@ Line 1: / Line 1: @@
+The GitHub resource for this protocol: https://github.com/zx0223winner/TreeTuner
 **Background**
@@ Line 337: / Line 339: @@
 MDNKYTSSAQNVLVLAQEQAKYFKHQAVGTEHLLLALAIEKEGIASKILGQ
 </code>
+Directory to renamed MMETSP: /misc/scratch2/###/###/mmetsp
 Then with the two renamed database available, you could merge then by 'cat'. Then build the new merged database via 'makeblastdb'. Then Blast them again.8-)
@@ Line 344: / Line 348: @@
 Finally, after using two different methods, we can touch on the topic we raised up at very beginning. Coarse and fine-tuning large phylogenetic datasets via reducing the redundancy and complexity.
-. **Fine-tuning**  Laura Eme (2012-14) written in Perl
+. **Coarse-tuning**: Let's start with the relatively simple one coarse-tuning via Treetrimmer (Maruyama et.al 2013)
+<code>
+ruby treetrimmer.rb sample/####_aligned_trimmed.newick sample/###_parameter_input.in sample/taxonomic_info.txt > ###_treetrimmer.newick
+</code>
+The "##..newick" and "###input.in" files can easily be prepared. The taxonomic_info.txt;however need to reformatted.
+<code>
+taxonomic_info.txt
+NP_563657	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis; Arabidopsis thaliana
+XP_002889406	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis; Arabidopsis lyrata; Arabidopsis lyrata subsp. lyrata
+</code>
+The taxonomic_info.txt can be created by acc2tax program. please read more from here:http://129.173.88.134:81/dokuwiki/doku.php?id=phylogeny_protocol3
+__Note: The acc2tax need the gene ID without version (e.g.NP_563657), so as the NCBI ID.__ Please find the usage of the program: http://129.173.88.134:81/dokuwiki/doku.php?id=taxonomy_recovery; http://129.173.88.134:81/dokuwiki/doku.php?id=phylogeny_protocol3
+<code>
+>WP_048801694.1	ATP-dependent Clp protease ATP-binding subunit [Leuconostoc citreum]GEK62024.1 ATP-dependent Clp protease ATP-binding subunit ClpC [Leuconostoc citreum]
+MDNKYTSSAQNVLVLAQEQAKYFKHQAVGTEHLLLALAIEKEGIASKILGQFNVTDDDIREEIEHFTGYGM
+</code>
+With the taxonomic_info.txt ready, you can get the tree file and another taxa file:
+<code>
+XP_026407875	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Ranunculales; Papaveraceae; Papaveroideae; Papaver; Papaver somniferum	2	4
+XP_034682772	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis; Vitis riparia	2
+</code>
+This tree give a rough tree diversity estimation.
+. **Fine-tuning**  Laura Eme (2012-14) written in Perl
 <code>
@@ Line 388: / Line 424: @@
 Based on the trimmed aligned seq, you can re-analysis more rigorous downstream IQ-tree analysis.
-. **Coarse-tuning**: Let's start with the relatively simple one coarse-tuning via Treetrimmer (Maruyama et.al 2013)
+Note: not all genes' species have taxa.This have nothing to do with the updates of NCBI taxonomy.
+The '0' in Gene name 'CP_0177652116_0_Stygamoeba_regulata_BSH-02190019' is not a NCBI taxid.
-<Last updated by Xi Zhang on Oct 6th,2021> upcoming
+<Last updated by Xi Zhang on Oct 6th,2021>