Estimating amino acid substitution models from genome datasets: a simulation study on the performance of estimated models.

Estimating parameters of amino acid substitution models is a crucial task in bioinformatics. The maximum likelihood (ML) approach has been proposed to estimate amino acid substitution models from large datasets. The quality of newly estimated models is normally assessed by comparing with the existing models in building ML trees. Two important questions remained are the correlation of the estimated models with the true models and the required size of the training datasets to estimate reliable models. In this article, we performed a simulation study to answer these two questions based on simulated data. We simulated genome datasets with different numbers of genes/alignments based on predefined models (called true models) and predefined trees (called true trees). The simulated datasets were used to estimate amino acid substitution model using the ML estimation methods. Our experiments showed that models estimated by the ML methods from simulated datasets with more than 100 genes have high correlations with the true models. The estimated models performed well in building ML trees in comparison with the true models. The results suggest that amino acid substitution models estimated by the ML methods from large genome datasets are a reliable tool for analyzing amino acid sequences.

Estimating amino acid substitution models for metazoan evolutionary studies.

Amino acid substitution models represent the substitution rates among amino acids during the evolution of protein sequences. The models are a prerequisite for maximum likelihood or Bayesian methods to analyse the phylogenetic relationships among species based on their protein sequences. Estimating amino acid substitution models requires large protein datasets and intensive computation. In this paper, we presented the estimation of both time-reversible model (Q.met) and time non-reversible model (NQ.met) for multicellular animals (Metazoa). Analyses showed that the Q.met and NQ.met models were significantly better than existing models in analysing metazoan protein sequences. Moreover, the time non-reversible model NQ.met enables us to reconstruct the rooted phylogenetic tree for Metazoa. We recommend researchers to employ the Q.met and NQ.met models in analysing metazoan protein sequences.

nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this article, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time nonreversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the nonreversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of data sets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the data set. Notably, for the recently published plant and bird trees, these nonreversible models correctly recovered the commonly estimated root placements with very high-statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate nonreversible models and rooted phylogenies from their own protein data sets. The data sets and scripts used in this article are available at https://doi.org/10.5061/dryad.3tx95x6hx. [amino acid sequence analyses; amino acid substitution models; maximum likelihood model estimation; nonreversible models; phylogenetic inference; reversible models.].

Lattice Expansion in Rb-Doped Hybrid Organic-Inorganic Perovskite Crystals Resulting in Smaller Band-Gap and Higher Light-Yield Scintillators.

Two-dimensional hybrid-organic-inorganic perovskite (2D-HOIP) lead bromide perovskite crystals have demonstrated great potential as scintillators with high light yields and fast decay times while also being low cost with solution-processable materials for wide energy radiation detection. Ion doping has been also shown to be a very promising avenue for improvements of the scintillation properties of 2D-HOIP crystals. In this paper, we discuss the effect of rubidium (Rb) doping on two previously reported 2D-HOIP single crystals, BA2PbBr4 and PEA2PbBr4. We observe that doping the perovskite crystals with Rb ions leads to an expansion of the crystal lattices of the materials, which also leads to narrowing of band gaps down to 84% of the pure compounds. Rb doping of BA2PbBr4 and PEA2PbBr4 shows a broadening in the photoluminescence and scintillation emissions of both perovskite crystals. Rb doping also leads to faster γ-ray scintillation decay times, as fast as 4.4 ns, with average decay time decreases of 15% and 8% for Rb-doped BA2PbBr4 and PEA2PbBr4, respectively, compared to those of undoped crystals. The inclusion of Rb ions also leads to a slightly longer afterglow, with residual scintillation still being below 1% after 5 s at 10 K, for both undoped and Rb-doped perovskite crystals. The light yield of both perovskites is significantly increased by Rb doping with improvements of 58% and 25% for BA2PbBr4 and PEA2PbBr4, respectively. This work shows that Rb doping leads to a significant enhancement of the 2D-HOIP crystal performance, which is of particular significance for high light yield and fast timing applications, such as photon counting or positron emission tomography.

QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.[Amino acid replacement matrices; amino acid substitution models; maximum likelihood estimation; phylogenetic inferences.].

Facile hydrothermal synthesis of MXene@antimony nanoneedle composites for toxic pollutants removal.

A new 2D transition metal carbides family noted that MXene with antimony (Sb) nano-needles composites have demonstrated potential applications for photocatalytic dye degradations applications. Single-step synthesis of novel structures two/one-dimensional MXene@antimony nanoneedle (MX@Sb-H) nanocomposite-based photocatalysts is produced employing hydrothermal technique. The preparations and characterizations were compared with hand mixture preparations of pure TiO2@Sb and MXene (MX@Sb-M). The crystallographic structure was identified employing X-ray diffraction (XRD) studies and main sharp XRD peaks were observed with diffraction angle with orientations planes for all three samples TiO2@Sb, MX@Sb-M and MX@Sb-H. The micro-Raman spectroscopy explored key vibration modes centered at 151.72 and 637.52 cm-1 corresponding to Ti and Sb hybrid composites respectively. Fourier transform infrared spectroscopy (FTIR) spectrum of functional group peaks at 609.16 and 868.80 cm-1 revealed Ti-OH/Sb-O-C stretching. The morphological investigations of horizontal growth for "Sb" nanoneedle on MXene nanosheets were explored by scanning electron microscopy (SEM). The degradation efficiency was calculated. The efficiency calculated were 27%, 38%, 68% and 82% for MB solution, TiO2@Sb added MB, MX-Sb-M added MB and MX-Sb-H added MB solution and the efficiency were 32%, 38%, 50% and 65% for pure RhB solution, TiO2@Sb added RhB, MX-Sb-M added RhB and MX-Sb-H added RhB solution. The photocatalytic activity of TiO2@Sb, MX@Sb-M and MX@Sb-H was examined. Among these MX@Sb-H nanocomposite was demonstrated the high photocatalytic action in expressions of rate stability of photocatalytic dye degradations.

Pure and Ce-doped spinel CuFe2O4 photocatalysts for efficient rhodamine B degradation.

Wastewater management is becoming a serious issue worldwide. To enhance the reuse of wastewater, one has to remove toxic pollutants present in it. High amount of dye is present in wastewater, and to remove these dyes is the large scope of this research. Herein, we report production of pure and Ce-doped copper ferrite via hydrothermal route. The synthesized nanoparticles were collected and analyzed by basic characterization techniques. The bandgap energy calculated for pure, 1% Ce, and 2% Ce-doped CuFe2O4 was found to be 2.77, 2.57, and 2.36eV, respectively. Reduction in bandgap was attributed to the doping element. The shape and size of pure and Ce-doped products were investigated using a scanning electron microscope. Agglomeration was observed in the pure copper ferrite sample. In the Ce-doped sample, agglomeration was clearly reduced and the 2% Ce-doped CuFe2O4 sample showed growth of small nanoparticles. They showed complete growth and were arranged in a uniform manner without agglomeration. The surface area of the 2% Ce-CuFe2O4 sample was found to be 65.89 m2/g with 7.02 nm pore diameter. The photocatalytic activity of the prepared material was observed for rhodamine B degradation. The pure and catalyst-added dye was exposed under visible light. The samples were tested for UV. The efficiency obtained for pure dye solution, pristine CuFe2O4-added, and 1% Ce and 2% Ce-doped CuFe2O4-added dye solutions were 48%, 50%, 66%, and 88% within 2 h of irradiation. The 2% Ce-doped CuFe2O4 sample showed excellent photocatalytic activity as the bandgap and morphology were enhanced by doping an appropriate ratio of Ce ions.

Flexible, ultra-stable and color tunable fluorescent films based on all inorganic perovskite quantum dots embedded in polymer.

Colloidal perovskite CsPbX3 (X = Cl, Br, I) nanocrystals (CPNCs)/polymers composites have attracted extensive attention due to their potential to be developed as flexible phosphor films for lighting applications. However, to maintain high quantum efficiency and photo stability of CPNCs in such composites remains a daunting challenge. Here, we have demonstrated a layered composite structure consisting of CPNCs and polydimethylsiloxane (PDMS) with multi-color emission and long-term stability. By tuning the molar ratio between CsPbCl1.58Br1.42 and CsPbBr1.35I1.65, flexible fluorescent films as down-converter layers with a high luminescent efficiency and a controllable color temperature spanning from 3194 K to 5901 K have been demonstrated. Furthermore, due to embedding inside such composites, the quantum efficiency of CPNCs exhibited negligible changes during seven months in ambient conditions. The carrier dynamics based on time-resolved photoluminescence (PL) and transient absorption spectroscopy reveal that the hot electron tunneling and trapping process are significant in the composite film. This work provides a good understanding of CPNC materials in complex composite for the development of flexible, robust, color controllable fluorescent films for lighting applications.

Development of a Spatial Decision Support System for Real-Time Flood Early Warning in the Vu Gia-Thu Bon River Basin, Quang Nam Province, Vietnam.

Vu Gia-Thu Bon (VGTB) river basin is an area where flash flood and heavy flood events occur frequently, negatively impacting the local community and socio-economic development of Quang Nam Province. In recent years, structural and non-structural solutions have been implemented to mitigate damages due to floods. However, under the impact of climate change, natural disasters continue to happen unpredictably day by day. It is, therefore, necessary to develop a spatial decision support system for real-time flood warnings in the VGTB river basin, which will support in ensuring the area's socio-economic development. The main purpose of this study is to develop an online flood warning system in real-time based on Internet-of-Things (IoT) technologies, GIS, telecommunications, and modeling (Soil and Water Assessment Tool (SWAT) and Hydrologic Engineering Center's River Analysis System (HEC-RAS)) in order to support the local community in the vulnerable downstream areas in the event of heavy rainfall upstream. The structure of the designed system consists of these following components: (1) real-time hydro-meteorological monitoring network, (2) IoT communication infrastructure (Global System for Mobile Communications (GSM), General Packet Radio Service (GPRS), wireless networks), (3) database management system (bio-physical, socio-economic, hydro-meteorological, and inundation), (4) simulating and predicting model (SWAT, HEC-RAS), (5) automated simulating and predicting module, (6) flood warning module via short message service (SMS), (7) WebGIS, application for providing and managing hydro-meteorological and inundation data, and (8) users (citizens and government officers). The entire operating processes of the flood warning system (i.e., hydro-meteorological data collecting, transferring, updating, processing, running SWAT and HEC-RAS, visualizing) are automated. A complete flood warning system for the VGTB river basin has been developed as an outcome of this study, which enables the prediction of flood events 5 h in advance and with high accuracy of 80%.

Light-Emitting Diodes with Cu-Doped Colloidal Quantum Wells: From Ultrapure Green, Tunable Dual-Emission to White Light.

Copper-doped colloidal quantum wells (Cu-CQWs) are considered a new class of optoelectronic materials. To date, the electroluminescence (EL) property of Cu-CQWs has not been revealed. Additionally, it is desirable to achieve ultrapure green, tunable dual-emission and white light to satisfy the various requirement of display and lighting applications. Herein, light-emitting diodes (LEDs) based on colloidal Cu-CQWs are demonstrated. For the 0% Cu-doped concentration, the LED exhibits Commission Internationale de L'Eclairage 1931 coordinates of (0.103, 0.797) with a narrow EL full-wavelength at half-maximum of 12 nm. For the 0.5% Cu-doped concentration, a dual-emission LED is realized. Remarkably, the dual emission can be tuned by manipulating the device engineering. Furthermore, at a high doping concentration of 2.4%, a white LED based on CQWs is developed. With the management of doping concentrations, the color tuning (green, dual-emission to white) is shown. The findings not only show that LEDs with CQWs can exhibit polychromatic emission but also unlock a new direction to develop LEDs by exploiting 2D impurity-doped CQWs that can be further extended to the application of other impurities (e.g., Mn, Ag).

Single-shot multi-view imaging enabled by scattering lens.

Imaging three-dimensional (3D) objects has been realized by methods such as binocular stereo vision and multi-view imaging. These methods, however, needs multiple cameras or multiple shots to get elemental images. In this paper, we develop a single-shot multi-view imaging technique by utilizing the natural randomness of scattering media. By exploiting the memory effect and uncorrelated point spread functions (PSF) among scattering media, we demonstrate that both stereo imaging with large disparity and up to seven-view imaging of a 3D object can be reconstructed from only one speckle pattern by deconvolution. The elemental images are consistent with 3D object projection and images taken by multi-shot imaging. Our technique provides a feasible method to capture multi-view imaging with short acquisition time and easy calibration.

Multicenter, randomized controlled, observer-blinded study of a nitric oxide generating treatment in foot ulcers of patients with diabetes-ProNOx1 study.

The aim of this multicenter, prospective, observer-blinded, parallel group, randomized controlled trial was to assess the safety and efficacy of EDX110, a nitric oxide generating medical device, in the treatment of diabetic foot ulcers in a patient group reflecting "real world" clinical practice compared against optimal standard care. Participants were recruited from ten hospital sites in multidisciplinary foot ulcer clinics. The ulcers were full thickness, with an area of 25-2,500 mm2 and either a palpable pedal pulse or ankle brachial pressure index > 0.5. Infected ulcers were included. Treatment lasted 12 weeks, or until healed, with a 12-week follow-up period. Both arms were given optimal debridement, offloading and antimicrobial treatment, the only difference being the fixed used of EDX110 as the wound dressing in the EDX110 group. 135 participants were recruited with 148 ulcers (EDX110-75; Control-73), 30% of which were clinically infected at baseline. EDX110 achieved its primary endpoint by attaining a median Percentage Area Reduction of 88.6% compared to 46.9% for the control group (p = 0.016) at 12 weeks in the intention-to-treat population. There was no significant difference between wound size reduction achieved by EDX110 after 4 weeks and the wound size reduction achieved in the control group after 12 weeks. EDX110 was well tolerated. Thirty serious adverse events were reported (12 in the EDX110 group, of which 4 were related to the ulcer; 18 in the control group, of which 10 were related and 1 possibly related to the ulcer), with significant reduction in serious adverse events related to the ulcer in EDX group. There was no significant difference in adverse events. This study, in a real world clinical foot ulcer population, demonstrates the ability of EDX110 to improve healing, as measured by significantly reducing the ulcer area, compared to current best clinical practice.

Single-shot large field of view imaging with scattering media by spatial demultiplexing.

Benefiting from the memory effect (ME) for speckle intensity correlations, only one single-shot speckle pattern can be used for the high-quality recovery of objects. However, ME gives a restriction to the field of view (FOV) for imaging with scattering media. Objects beyond the ME region cannot be recovered and produce unwanted speckle patterns, which cause reduction in the speckle contrast and recovery quality. Nevertheless, all the spatial information from a large object is embedded in a single speckle image. Here, we extract the spatial information from these unavoidable speckle patterns and enlarge the FOV of the imaging system with scattering media. Regional point spreading functions, which are fixed and only need to be recorded once for all-time use, are employed to recover corresponding spatial regions of an object by deconvolution. Then, an automatic weighted averaging in an iterative process is performed to obtain the object with significantly enlarged FOV. Our results present an important advancement of imaging techniques with strongly scattering media.

Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.

BACKGROUND: Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences. RESULTS: We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes. CONCLUSIONS: We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data.

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.

BACKGROUND: Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex. As a compromise, sub-optimal pre-calculated generic matrices are typically used for protein-based phylogeny. Sequence availability has now grown to a point where problem-specific rate matrices can often be calculated if the computational cost can be controlled. RESULTS: The most time consuming step in estimating rate matrices by maximum likelihood is building maximum likelihood phylogenetic trees from protein alignments. We propose a new procedure, called FastMG, to overcome this obstacle. The key innovation is the alignment-splitting algorithm that splits alignments with many sequences into non-overlapping sub-alignments prior to estimating amino acid replacement rates. Experiments with different large data sets showed that the FastMG procedure was an order of magnitude faster than without splitting. Importantly, there was no apparent loss in matrix quality if an appropriate splitting procedure is used. CONCLUSIONS: FastMG is a simple, fast and accurate procedure to estimate amino acid replacement rate matrices from large data sets. It enables researchers to study the evolutionary relationships for specific groups of proteins or taxa with optimized, data-specific amino acid replacement rate matrices. The programs, data sets, and the new mammalian mitochondrial protein rate matrix are available at http://fastmg.codeplex.com.

Surface-emitting red, green, and blue colloidal quantum dot distributed feedback lasers.

We demonstrate surface emitting distributed feedback (DFB) lasers across the red, green, and blue from densely packed colloidal quantum dot (CQD) films. The solid CQD films were deposited on periodic grating patterns to enable 2nd-order DFB lasing action at mere 120, 280, and 330 µJ/cm2 of optical pumping energy densities for red, green, and blue DFB lasers, respectively. The lasers operated in single mode operation with less than 1 nm of full-width-half-maximum. We measured far-field patterns showing high degree of spatial beam coherence. Specifically, by taking advantage of single exciton optical gain regime from our engineered CQDs, we can significantly suppress the Auger recombination to reduce lasing threshold and achieve quasi-steady state, optically pumped operation.

QMix: An Efficient Program to Automatically Estimate Multi-Matrix Mixture Models for Amino Acid Substitution Process.

The single-matrix amino acid (AA) substitution models are widely used in phylogenetic analyses; however, they are unable to properly model the heterogeneity of AA substitution rates among sites. The multi-matrix mixture models can handle the site rate heterogeneity and outperform the single-matrix models. Estimating multi-matrix mixture models is a complex process and no computer program is available for this task. In this study, we implemented a computer program of the so-called QMix based on the algorithm of LG4X and LG4M with several enhancements to automatically estimate multi-matrix mixture models from large datasets. QMix employs QMaker algorithm instead of XRATE algorithm to accurately and rapidly estimate the parameters of models. It is able to estimate mixture models with different number of matrices and supports multi-threading computing to efficiently estimate models from thousands of genes. We re-estimate mixture models LG4X and LG4M from 1471 HSSP alignments. The re-estimated models (HP4X and HP4M) are slightly better than LG4X and LG4M in building maximum likelihood trees from HSSP and TreeBASE datasets. QMix program required about 10 hours on a computer with 18 cores to estimate a mixture model with four matrices from 200 HSSP alignments. It is easy to use and freely available for researchers.

Effect of Dual-Organic Cations on the Structure and Properties of 2D Hybrid Perovskites as Scintillators.

Two-dimensional (2D) hybrid organic-inorganic perovskite (HOIP) crystals show promise as scintillating materials for wide-energy radiation detection, outperforming their three-dimensional counterparts. In this study, we synthesized single crystals of (PEA2-xBZAx)PbBr4 (x ranging from 0.1 to 2), utilizing phenethylammonium (C6H5CH2CH2NH3+) and benzylammonium (C6H5CH2NH3+) cations. These materials exhibit favorable optical and scintillation properties, rendering them suitable for high light yield (LY) and fast-response scintillators. Our investigation, employing various techniques such as X-ray diffraction (XRD), photoluminescence (PL), time-resolved (TR) PL, Raman spectroscopy, radioluminescence (RL), thermoluminescence (TL), and scintillation measurements, unveiled lattice strain induced by dual-organic cations in powder X-ray diffraction. Density functional theory analysis demonstrated a maximal 0.13 eV increase in the band gap with the addition of BZA cation addition. Notably, the largest Stokes shift of 0.06 eV was observed in (BZA)2PbBr4. The dual-organic cation crystals displayed >80% fast component scintillation decay time, which is advantageous for the scintillating process. Furthermore, we observed a dual-organic cations-induced enhancement of electron-hole transfer efficiency by up to 60%, with a contribution of >70% to the fast component of scintillation decay. The crystal with the lowest BZA concentration, (PEA1.9BZA0.1)PbBr4, demonstrated the highest LYs of 14.9 ± 1.5 ph/keV at room temperature. Despite a 55-70% decrease in LY for BZA concentrations >5%, simultaneous reductions in scintillation decay time (12-32%) may work for time-of-flight positron emission tomography and photon-counting computed tomography. Our work underscores the crucial role of dual-organic cations in advancing our understanding of 2D-HOIP crystals for materials science and radiation detection applications.

Modeling protein evolution with several amino acid replacement matrices depending on site rates.

Most protein substitution models use a single amino acid replacement matrix summarizing the biochemical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors that influence the substitution patterns. In this paper, we investigate the use of different substitution matrices for different site evolutionary rates. Indeed, the variability of evolutionary rates corresponds to one of the most apparent heterogeneity factors among sites, and there is no reason to assume that the substitution patterns remain identical regardless of the evolutionary rate. We first introduce LG4M, which is composed of four matrices, each corresponding to one discrete gamma rate category (of four). These matrices differ in their amino acid equilibrium distributions and in their exchangeabilities, contrary to the standard gamma model where only the global rate differs from one category to another. Next, we present LG4X, which also uses four different matrices, but leaves aside the gamma distribution and follows a distribution-free scheme for the site rates. All these matrices are estimated from a very large alignment database, and our two models are tested using a large sample of independent alignments. Detailed analysis of resulting matrices and models shows the complexity of amino acid substitutions and the advantage of flexible models such as LG4M and LG4X. Both significantly outperform single-matrix models, providing gains of dozens to hundreds of log-likelihood units for most data sets. LG4X obtains substantial gains compared with LG4M, thanks to its distribution-free scheme for site rates. Since LG4M and LG4X display such advantages but require the same memory space and have comparable running times to standard models, we believe that LG4M and LG4X are relevant alternatives to single replacement matrices. Our models, data, and software are available from http://www.atgc-montpellier.fr/models/lg4x.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

SUMMARY: Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. AVAILABILITY: http://www.atgc-montpellier.fr/ReplacementMatrix/ CONTACT: olivier.gascuel@lirmm.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/