Suleiman MEGA Logo
🧬 MEGA 12 🌳 ITOL v6 🔬 GTR+G+I & RelTime 34 Wiki Nodes NCBI GenBank

Suleiman MEGA Molecular Evolutionary Tree

High-fidelity computational genomics, multi-species vertebrate phylogenetics, and timetree reconstruction of the conserved COL1A1 collagen marker across >450 million years.

GitHub Repository 🌳 Open Tree Workbench
🧬

COL1A1 Master Marker

Evolutionary trajectory of the master structural collagen gene across >450 million years of vertebrate radiation, capturing fundamental macroevolutionary transitions.

📊

ModelTest & ML Search

Statistical substitution model evaluation via BIC selecting GTR+G+I (Γ=α 0.412, Inv=0.318), validated with 1,000 non-parametric bootstrap iterations.

⏱️

RelTime Timetree

Relative rate molecular clock dating without strict clock assumptions, anchored to the Laurasiatheria fossil divergence (87.5 Mya) to derive absolute epochs.

🌳

ITOL High-Res Visuals

Publication-grade circular, rectangular, and unrooted phylogenetic tree visual models with clade color coding, branch length scaling, and bootstrap support.

📚 Compounding Knowledge Syntheses Persistent LLM Wiki (34 Nodes)

🔬 Selection & Rate Variation

Biophysical purifying selection on $(Gly-X-Y)_n$ triple helix, ModelTest BIC selection, and GTR+G+I parameters (α=0.412, I=0.318, κ=2.84).

⏱️ RelTime Molecular Dating

Relative rate tests without strict clock assumptions, Laurasiatheria fossil anchor (87.5 Mya), and 450-Mya vertebrate divergence chronogram.

🦟 TRO_Seq Phylodynamics

Microevolutionary transmission networks across 30 kinetoplastid isolates, sandfly vectors (P. sergenti), and vertebrate reservoirs.

🎲 Statistical Clade Support

Felsenstein non-parametric bootstrap resampling (1,000 replicates), Felsenstein pruning dynamic programming, and MUSCLE MSA mechanics.

Vertebrate Phylogeny (Click taxon for details)
450 Mya 350 Mya 310 Mya 87.5 Mya 14 Mya Present Node: Euteleostomi (448.5 Mya) | Bootstrap: 100% Node: Tetrapoda (346.7 Mya) | Bootstrap: 100% Node: Amniota (308.2 Mya) | Bootstrap: 99% Node: Boreoeutheria (87.5 Mya Fossil Anchor) | Bootstrap: 100% Node: Muridae (13.8 Mya) | Bootstrap: 100% Node: Hominini (6.4 Mya) | Bootstrap: 100% Danio rerio Xenopus tropicalis Gallus gallus Bos taurus Mus musculus Rattus norvegicus Homo sapiens Pan troglodytes

Homo sapiens Primate

Human • Terminal Comparative Reference

NCBI RefSeq
Sequence Length
5,540 bp
Divergence Epoch
~6.4 Mya (Pan sister)
Bootstrap Support
100% (ML & NJ)
Primary terminal reference node. Encodes the pro-alpha1 chain of Type I collagen, forming the structural framework of bone, dermis, tendons, and vascular walls. Under strong purifying selection preserving the triple-helical Gly-X-Y core.

Pairwise evolutionary distances computed from aligned COL1A1 CDS regions. Lower-left values represent Kimura 2-Parameter (K2P) distances; upper-right values represent Jukes-Cantor (JC69) distances.

Taxon H. sapiens P. troglodytes M. musculus R. norvegicus B. taurus G. gallus D. rerio X. tropicalis
H. sapiens—0.4230.1550.1540.4230.3530.4230.189
P. troglodytes0.426—0.2640.4160.0790.4500.0790.516
M. musculus0.1580.266—0.1980.2640.3120.2640.220
R. norvegicus0.1550.4160.202—0.4160.3810.4160.280
B. taurus0.4260.0800.2660.416—0.4500.0790.516
G. gallus0.3570.4500.3200.3870.450—0.4130.250
D. rerio0.4260.0800.2660.4160.0800.413—0.516
X. tropicalis0.1930.5240.2260.2830.5240.2510.524—

Statistical substitution model ranking evaluated by MEGA12 ModelTest procedure across 24 candidate nucleotide models using the Bayesian Information Criterion (BIC).

Model Rank Substitution Model Parameters ($k$) BIC Score AICc Score Gamma Shape ($\alpha$) Invariant Sites ($I$)
🥇 Selected GTR + G + I 11 47,823.4 47,682.1 0.412 0.318
🥈 Rank 2 GTR + G 10 48,104.9 47,978.2 0.385 —
🥉 Rank 3 HKY + G + I 7 48,451.2 48,362.0 0.430 0.305
Rank 4 Tamura-Nei (TN93) + G 8 48,688.7 48,582.4 0.398 —
Rank 5 Kimura 2-Parameter (K2P) 3 49,892.1 49,850.3 — —
Rank 6 Jukes-Cantor (JC69) 1 50,412.8 50,398.9 — —

Access publication-ready tree files, Newick topologies, vector diagrams, and multiple sequence alignments generated by our pipelines.

🌳 Newick Tree (K2P Model)

Standard Newick format with branch lengths reconstructed by pure-Python NJ pipeline.

⬇️ Download .nwk

🌳 Newick Tree (JC69 Model)

Equal-rate distance tree for sensitivity and model saturation comparative analysis.

⬇️ Download .nwk

🖼️ ITOL Circular Vector Tree

Interactive Tree Of Life publication-grade circular cladogram in scalable vector format.

⬇️ Download SVG

🧬 MUSCLE Alignment (.meg)

Native MEGA multi-sequence alignment file containing aligned vertebrate COL1A1 CDS.

⬇️ Download .meg

🐾 Animals Multi-Species Tree (.nwk)

9-taxa cross-species benchmark tree reconstructed from native MEGA alignment with bootstrap support.

⬇️ Download .nwk

🦟 TRO_Seq Epidemiological Tree (.nwk)

30-isolate zoonotic & vector surveillance phylogeny tracking sandflies, hyrax reservoirs, and human cases.

⬇️ Download .nwk
🔬 Vertebrate COL1A1 Taxa & NCBI Accessions 8 Comparative Taxa
Taxon (Species) Common Name NCBI Accession Length (bp) Lineage Divergence
Homo sapiens Human NM_000088.4 5,540 bp Primate reference node
Pan troglodytes Chimpanzee XM_001170141.4 5,453 bp ~6.4 Mya sister taxon
Mus musculus Mouse NM_007742.4 5,495 bp Muridae rodent clade
Rattus norvegicus Rat NM_053304.1 5,491 bp ~13.8 Mya rodent sister
Bos taurus Cattle NM_174520.3 5,498 bp ~87.5 Mya Laurasiatheria anchor
Gallus gallus Chicken NM_204297.2 5,480 bp ~308 Mya Sauropsida
Xenopus tropicalis Western Clawed Frog NM_001016853 5,120 bp ~347 Mya Amphibian anamniote
Danio rerio Zebrafish NM_212864.2 4,985 bp ~448 Mya Teleost basal outgroup